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Poll: Republicans Gov. Brian Sandoval Beats Democrat Senate Majority Leader Harry Reid 53% to 43% in Hypothetical 2016 Nevada Senate Matchup
In a recent Harper Polling survey, the poll shows that in a hypothetical match 2016 match-up for the US Senate for Nevada Republican Gov. Brian Sandoval handily defeat Democrat Majority Leader Harry Reid by 10 points, 53% to 43%. The poll also showed that Gov. Sandoval destroys Reid among independents, 65%-28%. OUCH. Have the citizens of Nevada finally grown weary of Dingy Harry? One has to wonder whether the people of Nevada will have to wait until 2016 to rid themselves of Reid. If the GOP does not find a way to blow it, Republicans could take back the Senate in 2014 and Reid would lose is Majority Leader role. One would then have to ponder whether 74 year old Reid would stay in the Senate.
Full poll results can be read HERE (pdf)
Gov. Brian Sandoval leads Senate Majority Leader Harry Reid by 10 percentage points in a hypothetical 2016 U.S. Senate matchup, according to a new poll that represents the first public release of results in this potential race.
The survey, conducted by Harper Polling earlier this week, also shows, as other surveys do, Sandoval cruising to re-election (56-34) over Bob Goodman. The robo-survey of 602 statewide voters has a margin of error of 4 percent.
Sandoval crushes Reid among independents, 65-28. Reid's 55 percent unfavorable rating is all but fatal — you know, just as it was in 2010.
The NRO reminds us that Harry Reid has proven to be resilient against past challengers like in 2010 when Reid seemed vulnerable, but eventually defeated Republican candidate Sharron Angle by nearly 6 percentage points. However, popular Governor Brian Sandoval is not Sharron Angle. But if it does get to a 2016 Senate race between Sandoval and Reid and the polling is still as one sided toward the Nevada Governor, look for Reid to retire, he will be 80, rather than losing in an embarrassing swan song.
Posted August 1, 2014 by Scared Monkeys
2016 Elections, Brian Sandoval (NV-R), Harry Reid (D-NV), Polls, Senate, Senate Elections | no comments
Charles Krauthammer on Harry Reid's Secure Border Comment … "You've got to Wonder, Whether He's really on his Medication or Not."
Many legal American citizens have the same question …
Syndicated columnist Charles Krauthammer mocked Democrat Senate Majority Lead Harry Reid yesterday on 'Special Report' with regarding to Reid's comment that the Southern border was secure stating, When you hear Harry Reid saying the border is secure you've got to wonder, you know, whether he's really on his medication or not."
Well Harry, are you?
Click HERE or on pic to watch VIDEO at RCP
CHARLES KRAUTHAMMER: When you hear Harry Reid saying the border is secure you've got to wonder, you know, whether he's really on his medication or not. I mean, that is so detached from reality. We just saw at the beginning of the show the report from John Roberts — you get how many we have now? 60,000 — at least — kids who come over. And we're completely helpless. And it's the helplessness that I think is driving the president and the Democrats to accept. What they want is for the Republicans to be the one who would propose the change in the law because it looks so cruel.
MARA LIASSON: They did.
KRAUTHAMMER: And so the Republicans have played their role in this kabuki. The president will reluctantly accept it even though he talked initially about proposing it but then he got heat from his left which said you can't propose this. So it will work out. But the president has to have this stopped because it contributes to the story, showing all the other elements abroad and at home that his administration is incompetent, out of control and unable to control anything. And with this continuing he really can't tolerate that, his numbers will not survive and the party will be roundly thrashed in November and that's why he'll acquiesce to the change in the law.
Posted July 16, 2014 by Scared Monkeys
Charles Krauthammer, Democrats, Harry Reid (D-NV), Illegal Immigration, Liberals, Mexico, Open Borders - Border Security, Progressives, United States, WTF, You Tube - VIDEO | one comment
Democrat Majority Leader Harry Reid Says the United States-Mexican "Border Is Secure"
File this one under, ARE YOU KIDDING ME!!!
Okay America, who are you going to believe,
Baghdad Bob Harry Reid or your lying eyes? Democrat Senate Majority Leader Harry Reid of Nevada said Tuesday that the southern border was secure. Seriously, as a humanitarian crisis occurs on the US-Mexican borders as illegals pour over the borders, Reid says "the border is secure". What about this illegal child crisis that Democrats are looking to capitalize on, is that the sign of a secure border? How about those 50,000 unaccompanied youths and children who have illegally crossed the Texas border during the last few months? We have a porous southern border that is not just a humanitarian crisis, but a national security one and this lying Democrat leader says, don't look here, there is nothing to worry about. UNREAL.
However, Reid says he is against the bi-partisan proposed Cornyn-Cuellar bill that would allow unaccompanied minors to make a claim for asylum in the United States before an immigration judge within seven days of receiving a screening from the Department of Health and Human Services.
Of course Reid is against any bill that would remedy the crisis, its all about politics.
VIDEO – Roll Call
The Hill - Reid: Southern border is secure.
Senate Majority Leader Harry Reid (D-Nev.) on Tuesday asserted the southern border is secure despite the massive surge of illegal minors from Central America that has overwhelmed federal agencies.
"The border is secure," he told reporters after the Senate Democrats' weekly policy lunch. "[Sen.] Martin Heinrich [(D-N.M.)] talked to the caucus today. He's a border state senator. He said he can say without any equivocation the border is secure."
Reid said lawmakers need to worry less about border security and focus instead on President Obama's $3.7 billion request to help process the tens of thousands of children from Honduras, Guatemala and El Salvador who have been apprehended on the border.
Senator Dingy Harry is sounding an awful lot like Baghdad Bob did during the days of the War in Iraq when the US military was near the gates of Baghdad. Can anyone tell the difference between the two?
Posted July 16, 2014 by Scared Monkeys
Child Endangerment, Child Welfare, Corruption, Cover-Up, Democrats, Epic Fail, Gutter Politics, Harry Reid (D-NV), Illegal Immigration, Liars, Liberals, Mexico, Misleader, Moonbats, Obamanation, Open Borders - Border Security, Progressives, United States, WTF, You Tube - VIDEO | 2 comments
Democrat 'Unhinged' Insanity … Senate Majority Leader Harry Reid Blames Republicans For Russia Annexing Crimea
More proof Democrats are in serious trouble for the midterm 2014 elections … Senate Majority Leader Reid says Republicans are to blame for Russia's take-over of Crimea.
Some people have no shame, add Senate Majority Leader Harry Reid to that list. Sen. Harry Reid (NV-D) said Monday that Republicans helped Russia annex Ukraine's Crimea. Hmm, where is the outrage from the MSM over such a slanderous accusation? What kind of an irresponsible foll must one be to make such a comment. However, Reid has been making such outrageous comments like these for years and been getting a free pass. A spokesman for Republican House Speaker John Boehner called Senate Majority Leader Harry Reid "unhinged". That's an understatement.
This is what passes as leadership in the US Senate? It is hard to believe this man gets reelected, let alone is the Senate Majority Leader. That needs to change in 2014, Wake up America!
We need to play the blame game to distract from Obamacare and our parties failed president …
Senate Majority Leader Harry Reid said Monday that Republicans may have helped Russia annex Ukraine's Crimean Peninsula in a surprisingly sharp attack ahead of a test vote on a bill authorizing more U.S. sanctions on Russia and $1 billion in loan guarantees to Ukraine.
Outlining the Senate's agenda after a one-week recess, the Nevada Democrat said the first item would be the Ukraine bill that Republicans blocked just before lawmakers went on break. He urged Republicans to consider "how their obstruction affects United States' national security as well as the people of Ukraine" and said their delay of any congressional action "sent a dangerous message to Russian leaders."
"Since a few Republicans blocked these important sanctions last work period, Russian lawmakers voted to annex Crimea and Russian forces have taken over Ukrainian military bases," Reid said. "It's impossible to know whether events would have unfolded differently if the United States had responded to Russian aggression with a strong, unified voice."
As the Lonely Conservative aptly points out, Dingy Harry failed to mention that the bill the GOP blocked would have given Russia more control over the International Monetary Fund.
In other news, Harry Reid blamed Republicans for the mudslides in Washington state, the disappearance of the Malaysia airline in the Indian ocean and the kidnapping of the Lindbergh's baby.
Posted March 25, 2014 by Scared Monkeys
Congress, Democrats, Government, Gutter Politics, Harry Reid (D-NV), Liberals, Media, Media Bias, Moonbats, Obamanation, Politics, Progressives, Republican, Russia, Senate, Ukraine, United States, WTF | 3 comments
Democratic Senate Majority Leader Harry Reid Says Let 'We the People' Eat Obamacare … To Exempt Some of his Staff From Having to Buy Insurance Through Obamacare
If any law maker ever passes inflicts a law on the American people and does not have to abide by it themselves, should be thrown out of office. Enter Democrat Majority Leader Harry Reid who has exempted some of his staff from following the very law that Democrats passed along a partisan vote on the American people. No double standard here.
What, me accept Obamacare … are you crazy!!!
Democratic Senate Majority Leader Harry Reid, one of Obamacare's architects and staunchest supporters, is also the only top congressional leader to exempt some of his staff from having to buy insurance through the law's new exchanges.
Reid is the exception among the other top congressional leaders. GOP House Speaker John Boehner, House Democratic Leader Nancy Pelosi and Senate Republican Leader Mitch McConnell have all directed their staffs to join the exchange, their aides said.
In the charged atmosphere surrounding Obamacare, Reid's decision only gives Republicans more ammo to attack Democrats already suffering politically from the law's botched rollout.
Posted December 4, 2013 by Scared Monkeys
Barack Obama, Chicago-Style Politics, Democrats, Double Standard, Government, Gutter Politics, Harry Reid (D-NV), Healthcare, Healthcare.gov, Liberals, Misleader, Obamacare, Politics, Progressives, Senate | 2 comments
Harry Reid, the Senate Democrats, Barack Obama & Joe Biden's Nuclear Hypocrisy … Senate Goes Nuclear with Democrat Party Vote 52-48
Partisan Democrats end 225 years of precedent … Democrats just striped the protection of "We the People" who are in the minority.
Democrats were against it, before they were for it …
Yesterday, Democrats broke 225 years of precedent, when the U.S. Senate voted along Democrat partisan line 52-48 to invoke the so-called nuclear option allowing confirmation for most presidential nominees by simple majority. Some Democrats split with the party and voted against the change; however, the 52 votes were all of the Democrat party. Hmm, isn't how we got Obamacare? What this does is the Senate voted to severely limit the use of the filibuster, one of the few tools a minority party has in our representative democracy. This was nothing more than a "Naked Power Grab." As Dana Milbank writes, Congress wasn't broken before, it certainly is now. What Reid (D-NV) and his fellow Democrats effectively did was take the chamber of Congress that still functioned at a modest level and turn it into a clone of the other chamber, which functions not at all. They turned the Senate into the House.
The Senate vote Thursday to lower the barriers for presidential nominations should make it easier for President Obama to accomplish key second-term priorities, including tougher measures on climate change and financial regulation, that have faced intense opposition from Republicans in Congress.
The move to allow a simple majority vote on most executive and judicial nominees also sets the stage for Obama to appoint new top officials to the Federal Reserve and other key agencies — probably leading to more aggressive action to stimulate the economy and housing market. And it frees Obama to make changes to his Cabinet without the threat of long delays in the Senate before the confirmation of nominees.
Laura Ingraham discuses the "nuclear option" on 'The O'Reilly Factor'.
What complete Democrat HYPOCRISY!!!
Remember when Senate Barack Obama said he was against the "Nuclear" option in 2005? So why the sudden change of heart Obama? Maybe because as we saw with Obamacare, you are just a lair. Hmm, did Obama also run in 2012 on the notion that "if you like the rules of the US Senate you can keep them'? What a frigging hypocrite.
The Gateway Pundit has more on Harry Reid and Dems Overturn 1806 Senate Rule & Pass 'Nuclear Option.'
Senator Barack Obama in 2005 against the nuclear option
Senator Joe Biden in 2005 against the nuclear option. Take a good listen at what Biden says when he was in the minority.
Obama says this is not what the Founders intended … compilation of numerous Democrats who were against it, before they were for it.
Joe Biden calls it a "naked" power grab and says, "you will not be in the majority forever".
Establishment Republicans Surrender … House Passes Senate Bill to Reopen Government and Increase Debt Limit 285-144 … Senate Passes Bill 81-18
Speaker Boehner and GOP cave … In a country that already spends more than it takes it, irresponsible politicians kick the can down the road and raise the debt limit to spend even more money that America does not have.
Tonight the US Senate and House of Representatives passes the Senate led bill to end the partial government shutdown and increase the debt limit. The Senate passed the bill 81 to 18 and the House voted in favor of it 285 to 144. Incredibly, not one Democrat in the House or Senate voted against raising the debt on "We the People". Imagine that? CNN reports that President Barack Obama will sign it immediately. The director of the Office of Management and Budget said that federal workers should expect to return to work Thursday morning. Hmm, does this mean that open air monuments will be open to of military veteran heroes?
In Obama's speech tonight there was no reference to the GOP as terrorists or hostage takers … where is the evil rhetoric Mr. President?
Congressional Republicans conceded defeat on Wednesday in their bitter budget fight with President Obama over the new health care law as the House and Senate approved last-minute legislation ending a disruptive 16-day government shutdown and extending federal borrowing power to avert a financial default with potentially worldwide economic repercussions.
With the Treasury Department warning that it could run out of money to pay national obligations within a day, the Senate voted overwhelmingly Wednesday evening, 81 to 18, to approve a proposal hammered out by the chamber's Republican and Democratic leaders after the House on Tuesday was unable to move forward with any resolution. The House followed suit a few hours later, voting 285 to 144 to approve the Senate plan, which would fund the government through Jan. 15 and raise the debt limit through Feb. 7.
Most House Republicans opposed the bill, but 87 voted to support it. The breakdown showed that Republican leaders were willing to violate their informal rule against advancing bills that do not have majority Republican support in order to end the shutdown. All 198 Democrats voting supported the measure.
From Business Insiders, Here's The Bill That's Going To End The Government Shutdown And Raise The Debt Ceiling.
A list of the 18 Republican Senators who voted against the Bill that will raise the debt and continue the out of control, drunken spending of politicians.
Coburn (R-OK)
Cornyn (R-TX)
Crapo (R-ID)
Cruz (R-TX)
Enzi (R-WY)
Grassley (R-IA)
Heller (R-NV)
Johnson (R-WI)
Lee (R-UT)
Paul (R-KY)
Risch (R-ID)
Roberts (R-KS)
Rubio (R-FL)
Scott (R-SC)
Sessions (R-AL)
Shelby (R-AL)
Toomey (R-PA)
Vitter (R-LA)
UPDATE I: All the House, Senate and President have done is kick the can down the road and solve nothing. No one wants to make the tough and responsible decisions because we have politicians who care more about their power and their agenda than they do "We the People" or the United States of America. Honestly, who in their right mind thinks that a country can continue to borrow billions of dollars a day and actually sustain itself?
Million Vet March on Sunday, October 13, 2013 … Open the WWII Memorial to Our Hero Veterans!
March against tyranny and for our Veterans …
March with our veterans and the heroes that have made America free on Sunday, October 13, 2013 in Washington, DC. The Million Vet March is going to take place t 9:00 a.m. at the World War II Memorial. Who has been disgusted by the actions of Barack Obama and our government in closing down open air memorials that are normally open 24-7 like the WWII Memorial to Our Greatest Generation? Who does this? What kind of reprehensible, uncaring, malicious government actually closes an open air monument and prevents aged vets from seeing the memorial that honors them and their fallen soldiers?
What kind of a government does this to inflict pain on the people to win political points? How exactly does Barack Obama square these actions with laying a wreath at The Tomb of the Unknowns at Arlington National Cemetery on Veteran's Day?
Go to VET MARCH.com for all the details.
I want you to circle the date of Sunday, October 13, 2013.
And then I want you to help "circle the wagons" on that day to help protect and defend our brave veterans who risked their lives for our freedom – and now are being barred from visiting the memorials erected to honor their deeds.
In a mean-spirited fit of selfish anger, Barack Obama has shut down our nation's war memorials. And he has declared open war on our honored veterans!
The World War II memorial … the Vietnam Veterans Memorial … the Korean War Veterans Memorial – Obama has shut them all down to force his will on the House of Representatives and frankly, to get revenge on the American people who oppose Obamacare and his other naked power grabs.
Let's put it plainly: Barack Obama is behaving like a vicious tyrant. And if he succeeds in this assault on the democratic system, the Republic we love is at mortal risk. It's just that simple.
That's why I am asking you now to take two decisive moves to show Barack Obama, Harry Reid, Nancy Pelosi – and all of their oppressive ilk in Washington – that "We the People" are still in charge. And we won't rest until we take back our memorials and monuments!
Mark Levin to Barack Obama Says You Lay One Damn Hand on WW2 Vets and I'LL BRING HALF A MILLION PEOPLE TO THAT DAMN MEMORIAL!
Posted October 11, 2013 by Scared Monkeys
Abuse of Power, America - United States, Barack Obama, Chicago-Style Politics, Community Agitator, Freedom - Liberty, Government, Gutter Politics, Harry Reid (D-NV), heroes, Military, Obamanation, Politics, Restoring America, We the People, WTF | 4 comments
Sen. Harry Reid (D-NV) Asked "But If You Wanted to Help One Child With Cancer, Why Wouldn't You Do It?" His Response, "Why Would We Want To Do That"
What ever happened to Democrats were for the Children? Democrat Senator Majority Leader Harry Reid and Democrats let America know just how little they care about children with cancer …
Just how little do Democrats care more about playing politics than they do actually caring about the children with cancer of "We the People," one needs to look no further than the video below of Harry Reid being asked by a CNN reporter. Reid was asked, "but if you wanted to help one child with cancer, why wouldn't you do it?" The reporter was referring to the fact that the GOP controlled House was passing a bill to add funding for the National Institute of Health (NIH), national parks and veterans.
Harry Reid's response … "WHY WOULD WE WANT TO DO THAT".
Isn't that special. So we can now see just how little Obamacare really is about patient care and more about control. If Democrats really cared about the well being of individuals, they would pass a piecemeal bill that would include aiding cancer children. But no, instead they would rather play hard ball politics and defend Obamacare, a health care law that a majority of Americans do not want and most want it repealed. But Democrats would rather protect Obamacare at all cost than help children with cancer. Hmm, and I thought Democrats were supposed to be compassionate?
Posted October 4, 2013 by Scared Monkeys
Barack Obama, Cancer, Chicago-Style Politics, Child Endangerment, Child Welfare, Democrats, Double Standard, Government, Gutter Politics, Harry Reid (D-NV), Healthcare, Liberals, Obamacare, Obamanation, Partisan hack, Politics, Politics of Fear, Progressives, WTF, You Tube - VIDEO | 3 comments
House Votes to Delay Obamacare 231-192 … Back to the US Senate and Harry Reid
The US House of Representatives votes to delay Obamacare by one year by a 231 to 192 margin. However, Nancy Pelosi (D-CA) had more important things to do like not show up for the vote. The vote once again puts the ball back in the court of the US Senate. However, Senate Majority Leader Harry Reid has said he will make no compromises.
House Republicans forced through a short-term government funding bill that delays Obamacare and permanently repeals a tax on medical devices, setting up their most dramatic face-off ever with President Barack Obama and Senate Democrats.
The vote to delay Obamacare was 231-192, with two Republicans voting against the bill, while two Democrats supported it. The Republicans opposed to the bill were New York Reps. Chris Gibson and Richard Hanna, and the Democrats who supported the measure were North Carolina Rep. Mike McInytre and Utah Rep. Jim Matheson.
"The House has again passed a plan that reflects the American people's desire to keep the government running and stop the president's health care law," Boehner said in a post-vote statement. Repealing the medical device tax will save jobs and delaying the president's health care law for all Americans is only fair given the exemptions the White House has granted to big businesses and insurance companies."
He added: "Now that the House has again acted, it's up to the Senate to pass this bill without delay to stop a government shutdown."
House sends stopgap to Senate hours before shutdown (Video).
The high-stakes GOP move intensifies a game of chicken with Senate Democrats with just 48 hours to go before the lights could go out on the federal government.
The White House threatened to veto the measure, while Senate Majority Leader Harry Reid (D-Nev.) proclaimed it dead in the upper chamber.
The imminent deadline, combined with the prolonged impasse, has led some lawmakers to predict a shutdown is all but inevitable.
The Lonely Conservative, as myself, are surprised at the GOP's not backing down on the Obamacare/continuing resolution fight. I thought for sure Boehner and the establishment Republicans would have caved at this point. However, Senate Majority Leader Harry Reed is not backing down either and is pretty much taking the my way or the highway approach.
Much more at The American Thinker and the ultimate question ahead of a pending government shutdown … who will blink?
Posted September 29, 2013 by Scared Monkeys
Barack Obama, Community Agitator, Congress, Conservatives, Democrats, Divider in Chief, Harry Reid (D-NV), Healthcare, Misleader, Obamacare, Obamanation, Obamatax, Republican, Senate | no comments


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JOHN BOEHNER: My instinct is that we have -- a leadership table -- that reflects -- the broad -- group of members that are in our conference.
DIANE SAWYER: So, that says Tea Party?
JOHN BOEHNER: It says I want to make sure they represent -- the broad interest of all of our members. We're gonna have --
DIANE SAWYER: But it's fine with you? For sure?
JOHN BOEHNER: Whoever the members elect -- I'm going to serve with. And serve with successfully.
DIANE SAWYER: I think your instinct says that you are in no way going to answer my question.
JOHN BOEHNER: That'd be correct. (LAUGH) I should have just given you the Boehner shrug. All of the print reporters know what that means.
DIANE SAWYER: It means try as you might?
JOHN BOEHNER: I have no intention of answering that question (LAUGH)
DIANE SAWYER: It's a great gesture.
JOHN BOEHNER: I never even knew it. The reporter's all know it, oh they all got it and someone finally told me somebody described it as the Boehner shrug.
DIANE SAWYER: I'm going to try it, I'm going to try and steal it. Do it again.
JOHN BOEHNER: It's got everything -- eyebrows, shoulders.
DIANE SAWYER: Thanks again.


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How would you adapt Mass Effect into a movie?
View Single Post
May 1 2013, 11:25 AM
Rear Admiral
Location: UK
Re: How would you adapt Mass Effect into a movie?
The intro works fine for a game because it's immersive. But directly translate that onto the screen and you have a series of exposition dump conversations that have little to nothing to do with the plot. You just can't do it that way and expect the audience to keep up (see:
'Golden Compass'
Also keep in mind that the game slowly immerses you in the word, drip feeding background information here and there and even provides a whole codex of information for further details. A movie doesn't have the luxury of time to do it that way (nor of course is the codex an option.
Actually, let's take a look for ourselves: -
So we go from an out of context conversation about Shepard, to a text crawl, to a nice building musically supported crescendo showing off the Normandy and out main character which, to be fair you probably just spent upwards of 5 minutes creating (not so if this were a movie.)
Next, after Nihlus's introduction it's established that he's not part of the crew but an observer from something called the council. There is implicit distrust regarding this arrangement. Then we get a conversation about how mysterious our assignment is. Spectres are mentioned twice.
After a brief audio only introduction to Anderson, we're told to meet him down in the comm room. What follows are two optional conversations (I actually had a hard time finding a video clip that actually includes them!) that tells us about Turians, the First Contact War, Spectres, Normandy's function as a stealth ship, Spectres, some vague background about Anderson, more paranoia about the mission, Spectres, the council, Spectres, Shepard's background, Spectres, C-Sec, Spectres, Spectres, Spec--seriously, you could make a drinking game out of how often Spectres are mention in the first 10 minutes!
So yeah, we haven't even gotten to the comm room yet and already we're half way up to speed on the ME universe. Speaking of which, our conversation with first Nihlus then Anderson covers Eden Prime, humanity's rapid expansion, the fact their newcomers to the galaxy and the true nature of our mission (that mystery lasted all of 3 minutes!) Then things really ramp up and we're told about protheans their technology & sudden mysterious extinction, mass relays, the citadel, the beacon, the Mars archive, the attican traverse, the terminus systems...oh and hey, spectres!
Cut to plot twist #1 and our first glimpse of a reaper then we're off to Eden Prime....
Now don't get me wrong, it's a good intro that sets the tone very well and introduces the main character as well as Joker & Alenko, capturing their nascent personalities quite well. However, half it's purpose is to intoduce the player to the conversation wheel and movement controls (BTW, I really wish ME3 had done this.) As and interactive experience a game player is more inclined to go at their own pace as they get to grips with everything around them. Try doing this in a movie and all you'll get is a bunch of talking heads and a very bored audience.
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Link Between Worlds 5 Points Clear the first 5 levels! Medal Stats.
Vandal! 10 Points Manage to cut off the chandelier. Medal Stats.
Tick Her Off! 25 Points Deal enough damage to make the hydra fly. Medal Stats.
The Green Death 5 Points Survive the second encounter. Medal Stats.
Into The Darkness 5 Points Survive the first encounter. Medal Stats.
The Void 5 Points Begin the game. Medal Stats.
Bat Crush 10 Points SMASH a bat with blocks Medal Stats.
BE NOBODY 100 Points Yay, you completed the whole demo! You dissident! Medal Stats.
An Act of Activation 50 Points Complete the "Activating iEye" levels Medal Stats.
Slidewalking 25 Points Complete the "Slidewalk" levels Medal Stats.
Total Medals Earned: 226 (From 61 different games.)


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Climate Change in Europe & Central Asia
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North Brunswick Car DealerChange City
North Brunswick Car Dealer
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The North Brunswick car dealerships directory at Autobytel.com also features some great information in the form of reviews and ratings. See what previous customers of North Brunswick car dealers had to say about their experiences. These appraisals of North Brunswick car dealerships can be an effective way to figure out which dealership you should choose.


text:
Geographic Information Systems use software tools to gather, transform, manipulate, analyze, and produce geospatial data related to the surface of the earth.
Through a general-fund appropriation, ITD provides the hosting infrastructure and a product coordinator for the North Dakota GIS Hub. Database administrators, web application developers, web presentation developers, and system administrators all contribute to provide a reliable, scalable, and secure environment. The GIS Hub itself is the result of many more people working together through a GIS Statewide Alliance.
ITD's online Work Management System (WMS) may be used to submit a "Software Dev/GIS/PM/QA" Service Request.
For GIS-related issues, follow the GIS Incident Submission Guidelines.
Mark your calendars for the 2015 ND GIS Users Conference.
A GIS story map is just one of the many ways North Dakota utilizes GIS.
The Information Technology Department is sponsoring a workshop for ArcGIS users, as part of Visual ND.
The GIS Hub database environment has recently been upgraded. Although this upgrade applies mostly to state agencies, it might be interesting for some folks to know that the upgrade consisted of moving to new servers, upgrading the version of multiple Oracle instances, upgrading the version of multiple geodatabases, and upgrading the version of...
The North Dakota GIS Users Conference was a successful event with over 195 registered attendees from state agencies, counties, cities, higher education, utilities, and the private sector. The conference was held at the very nice Alerus Center in Grand Forks. The first keynote presentation, "Unmanned Aircraft: Turning Potential into Reality" was...
The GIS Strategic Plan has been updated for the 2013-2015 Biennium. To view the
The ND GIS User's Conference is approaching fast. Mark your Calendar with the following important dates:
The Conference Planning Committee is proud to announce two keynote speakers for the 2013 North Dakota GIS Users Conference: James Fee of Spatially Adjusted and Mark Askelson of the University of North Dakota.
ArcGIS Online (AGO) is a cloud-based solution from Esri that can be utilized to share data, services, maps, and applications.
In 2012 the North Dakota GIS Technical Committee (GISTC) developed a Historical Imagery Pilot Project to determine the feasibility and cost of creating one or more statewide and regional aerial imagery datasets that pre-date the 1995-1998 USGS DOQQs. This publicly available imagery will be used by multiple state agencies for change detection and...
Thank you so much, best help around!!
Copyright © 2015 North Dakota Information Technology Department - ITD
Use Adobe Reader to view, print and collaborate on PDF files.


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Green Beans And Goat Cheese Salad
23 Sep 2009
|Green beans
|4 1⁄2 Pound, ends trimmed
|Black pepper
|To Taste
|Olive oil
|1 1⁄2 Cup (24 tbs) (1 Cup Plus 2 Tablespoons)
|Chopped toasted pecans
|2 Cup (32 tbs)
|White wine vinegar
|3⁄4 Cup (12 tbs)
|Grated hard goat cheese/Imported parmesan
|1 1⁄2 Cup (24 tbs)
|3 Clove (15 gm), crushed
Steam green beans about 7 to 9 minutes, until crisp tender.
While beans are cooking, combine oil and vinegar and beat.
Add garlic and pepper.
Mix drained, warm beans with dressing and allow to sit about 10 minutes, longer if desired.
If beans will not be served within an hour or two, refrigerate, but return to room temperature before serving.
Just before serving, sprinkle beans with toasted pecans and grated cheese.
NOTE TO COOK: Carry marinated beans to party either in serving dish covered tightly with plastic wrap or in storage container.
Carry grated cheese and toasted pecans in separate containers.
Just before serving, finish dressing salad with cheese and pecans.
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Green Beans And Goat Cheese Salad Recipe


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2015-16 Middle School Handbook
Hatzic Middle will be having a football team for the 2015/16 school year. There will be a meeting on Thursday the 26th at 7 pm at the school. Football @ a Hatzic will be for next year's grade 7,8, and 9's. Fee: $125.
Amazing art done by Mrs. Lewington's Grade 10, 11 and 12 Art Class.
(Left to right: Breanna Fredrick McLean grade 10, Ciara Sater grade 10, Brooke Banman grade 12, Hannah Mah, grade 11)
Mr. Mill's contribution and efforts didn't stop when he retired from Hatzic. He has continued to support our school since then and we would like to take a moment and just say thank you! The most recent addition to our school generously donated by Mr. Mills is this beautiful piano.
The Leadership students of Hatzic honors all those who have served our country.
Homework Club is up and running! Students will be able to access homework club in the Aboriginal Room on Tuesdays and Thursdays. A late bus will promptly pick students up at 4:30pm.
Hatzic Middle is a comprehensive high school located in rural Mission, approximately 4 km east of the City of Mission, British Columbia, Canada. Overlooking the Fraser River with the Westminster Abby in the background, Hatzic Middle is situated in a beautiful location. Our 800 plus students come from both city and rural areas, bringing with them diverse educational interests and challenges. Our academic year is from September to June with students in Middle School (Grades 7 - 9).
Check My Mark Parent Login (recommended browser: Google Chrome)
The Middle School Crusader Blog Page
Fruit and Vegetable Program Opt Out Form
Parents - Please remember to call the office at 604.826.3651, within 48 hours, if your child will be absent, or if your child has an appointment. Any student that does not have a parent's permission to be excused will be marked away with an unexcused absence. Also, please take note that we DO NOT accept email or text messages, a parent must call in.
When registering, please bring a copy of the student's last report card, a birth certificate and a document containing your address (proof of residency)with you. Registration Forms may be found here and course selection forms may be found here.
Families are advised that registration of students who will be seeking bus transportation must do so, in person at the School District Office at 33046 Fourth Avenue during regular business hours 8:00am – 4:00pm M-F. If you are unavailable during those hours, alternate arrangements can be made by calling 604.826.6286 ext. 3246
Students that qualify to use district transportation services but who have not registered by June 30th will not be guaranteed a seat on a bus. Any registrations received after the June 30th deadline will incur a 20% surcharge fee.
Parents/guardians are advised to listen to one of the following radio stations for updates on weather conditions, with winter weather approaching:
Decisions about school schedules and bus route changes are almost always made in the early morning before school. This allows for the most current weather information to factor into the decision. This information is communicated immediately, generally before 6:30 a.m., using the methods above. Click on the snowman to get redirected to the latest news:
Students may use these devices before school, after school and during the lunch hour. Devices may not be permitted in the classroom without teacher permission.
Hatzic Middle School
34800 Dewdney Trunk Rd
Mission, BC V2V 5V6
Tel: 604.826.3651
Fax: 604.820.9209
email: Office
Shirley Gibson
email: Shirley Gibson
Andrew Merry
Grad Program
Grades 10 - 12
email: Andrew Merry
Joe Heslip
Grad Program & Grad Program Counsellor
Grades 10 - 12
email: Joe Heslip
Wayne Chow
Middle School
Grades 7 - 9
email: Wayne Chow
Year at a Glance
November 10 - Remembrance Day Assemblies
November 11 - Remembrance Day (school not in session)
November 17 - G.W. Cooke Awards (at HPSS, Clarke Theater, 7pm)
November 18 - PAC Gaming Fund Presentation (3:10pm in the Library)
November 21 - 11:30am Dismissal (Half-day assessment)
November 24 - Assembly for grades 9 - 11
November 25 - PAC Menchie's sale ($2.50 at lunch)
December 1-4 - Scholastic Book Sale (in Library)
December 4 - Parent-Teacher Conferences (3:20pm-5pm/6pm-8:30pm)
December 5 - School not in session
December 22 - January 5 - WINTER BREAK
January 27 & 28 - Final Exams
January 30 - School not in session
February 2 - English 12 & Social Studies 11 Provincial Exams
February 3 - Communications 12 Provincial Exam
February 4 - Grade 9 Immunizations
February 9 - Family Day - School not in session
February 13 - Pro-D Day - School not in session
February 12 - 19 - Report Card Pick-up (between 1-4)
March 16 - 20 - Spring Break
April 3 - Good Friday - School not in session
April 6 - Easter Monday - School not in session
April 9 - English 12, English10, Science 10 & Math 10 Provincial Exams
April 10 - Social Studies 11, Science 10 & Math 10 Provincial Exams
April 17 - 11:30am Dismissal (Half-day assessment)
April 30 - Parent-Teacher Conferences (3:20pm-5pm/6pm-8:30pm)
May 1 - School not in session
May 15 - Students not in session
May 18 - Victoria Day - Students not in session
June 5 - Hatzic Prom
June 13 - Hatzic Commencement
June 18 - Final Day of Regular Classes
June 19-24 - Provincial Exams
June 26 - Report Card Pick up (9am - 2pm)


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realmagick.com The shrine of knowledge.
Sports Radio Satellite
A selection of articles related to sports radio satellite.
Original articles from our library related to the Sports Radio Satellite. See Table of Contents for further available material (downloadable resources) on Sports Radio Satellite.
- More Group Mind Basics (GM2)
- The similarities between the function of a two-way radio and the human body can be quite surprising. The body/mind constantly emits all aspects of our internal state to the environment, and in turn receives inputs from the world in the same manner. When we...
Mind >> Telepathy and Group Mind
- Survivalists' Guide for the New Millennium: Chapter 3
- WAKE UP, GET DRESSED & MOVE OUT The search for Truth and meaning that occasionally marked the philosophies of the ancient world, appears to be in a state of serious decline in the present day. In our institutions of psychology and philosophy, there is...
Philosophy >> Survivalists Guide for the New Millennium
- Getting Up Again - A Story of Healing with Phosphorus and Anacardium
- Hope for the future gives life color and meaning. Having a body you can rely on is very important. In many cases the condition of the temple of our soul is a major key to happiness. And what makes healing so satisfactory is that the restoration of health...
Body Mysteries >> Homeopathy
- Yom Kippur
- Yom Kippur is the day when God handed to Moses the second set of the Ten Commandments. This occurred after the completion of the second 40 days of guidance from God.
Religions >> Judaism
- Beth Moore
- Beth Moore, founder and pastor of internationally known Living Proof Ministries, was born Wanda Elizabeth Green on June 16, 1957 in an army base at Green Bay, Wisconsin. Beth is the fourth of five children and was raised in Arkadelphia.
>> Modern Science
- The Elements of Color Magick
- "Color is the place where our mind and the universe meet each other." Paul Cezanne In magick colors represent a certain energy, goal, person (someone you're working for) or a non-physical being (deity, spiritual force). The magickal color meanings...
Symbology >> Colorology
Sports Radio Satellite is described in multiple online sources, as addition to our editors' articles, see section below for printable documents, Sports Radio Satellite books and related discussion.
Suggested Pdf Resources
- 17.4 Sports on Satellite Radio. As of August 2010, satellite radio had available 19 sports radio channels: 10 on.
- www.rkma.com
- CGC 11 ECONOMIC IMPACT Rls
- Jul 29, 2011 included SIRIUS Satellite Radio, Sporting News Radio, Fox Sports Radio, KNBR, WHB Radio and KGME Radio.
- www.tahoecelebritygolf.com
- A STUDY ON SPORTS A STUDY ON SPORTS - KLAS Sports Radio
- KLAS Sports Radio is a national radio station that focuses its programming on sports and .. Mega JAMZ BBC and satellite radio are also. IRIE FM.
- www.klassportsradio.com
- Welcome to the world of Satellite Radio
- SIRIUS CHANNEL LINEUP. Welcome to the world of Satellite Radio. COMMERCIAL-FREE MUSIC.
- www.siriusxm.com
- Yahoo! Sports and Gow Broadcasting Hit the Radio Airwaves with
- Aug 1, 2011 Sports Radio.
- radiotraque.imca.fr
Suggested News Resources
- Tim Brando brings a little Shreveport to The Big Dance
- Simulcast on Yahoo Sports Radio, satellite radio and the digital-cable CBS Sports Network, "The Tim Brando Show" is at its heart an always-enthusiastic celebration of college sports. All sports, really.
Suggested Web Resources
- Welcome to the world of satellite radio - SiriusXM Radio
- What Is Satellite Radio? It's like nothing you've ever heard before. Imagine just about every kind of music – commercial-free.
- www.siriusxm.com
- Sirius XM College Sports Nation - SiriusXM Radio
- www.siriusxm.com
- The Score Satellite Radio - Wikipedia, the free encyclopedia
- At Team Sports we put the 'eye' in Team cuz most people can't see beyond the 'I' in individual.
- en.wikipedia.org
- Fox Sports Radio - Wikipedia, the free encyclopedia
- en.wikipedia.org
- XM Radio vs Sirius Radio
- www.radiosatellite.org
Great care has been taken to prepare the information on this page. Elements of the content come from factual and lexical knowledge databases, realmagick.com library and third-party sources. We appreciate your suggestions and comments on further improvements of the site.
Sports Radio Satellite Topics
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What does CHAOS stand for?
What does CHAOS mean? This page is about the various possible meanings of the acronym, abbreviation, shorthand or slang term: CHAOS.
We've found a total of 31 definitions for CHAOS:
Filter by: Sort by:PopularityAlphabeticallyCategory
Create Havoc Around Our Systemtm
Christ Has All Our Solutions
Cyber Holistic Autonomous Orbiting Sever
Christians Hanging And Out Serving
A Chief Has Arrived On Scene
Cohesively Hampering Alterations For Ordered Stability
What does CHAOS mean?
- chaos, pandemonium, bedlam, topsy-turvydom, topsy-turvyness(noun)
- a state of extreme confusion and disorder
Still can't find the acronym definition you were looking for? Use our Power Search technology to look for more unique definitions from across the web!
"CHAOS." Abbreviations.com. STANDS4 LLC, 2015. Web. 1 Jul 2015. <http://www.abbreviations.com/CHAOS>.


text:
Structural variations (SVs) in genomes are commonly observed even in healthy individuals and play key roles in biological functions. To understand their functional impact or to infer molecular mechanisms of SVs, they have to be characterized with the maximum resolution. However, high-resolution analysis is a difficult task because it requires investigation of the complex structures involved in an enormous number of alignments of next-generation sequencing (NGS) reads and genome sequences that contain errors.
We propose a new method called ChopSticks that improves the resolution of SV detection for homozygous deletions even when the depth of coverage is low. Conventional methods based on read pairs use only discordant pairs to localize the positions of deletions, where a discordant pair is a read pair whose alignment has an aberrant strand or distance. In contrast, our method exploits concordant reads as well. We theoretically proved that when the depth of coverage approaches zero or infinity, the expected resolution of our method is asymptotically equal to that of methods based only on discordant pairs under double coverage. To confirm the effectiveness of ChopSticks, we conducted computational experiments against both simulated NGS reads and real NGS sequences. The resolution of deletion calls by other methods was significantly improved, thus demonstrating the usefulness of ChopSticks.
ChopSticks can generate high-resolution deletion calls of homozygous deletions using information independent of other methods, and it is therefore useful to examine the functional impact of SVs or to infer SV generation mechanisms.
Today, next-generation sequencing (NGS) technologies are essential tools in genome analysis, because they enable us to simultaneously obtain sequences of up to hundreds of billions of base pairs [1]. These technologies enable the characterization of not only small variations such as single-nucleotide polymorphisms (SNPs) but also large-scale mutations such as insertions, deletions, tandem duplications, and inversions. Mutations of these types are collectively called structural variations (SVs) and are frequently observed even in healthy individuals [2-4]. Because SVs affect a much larger portion of genomes than small variations, including SNPs, they have a great impact on biological functions.
Current NGS methods can sequence paired reads, which are pairs of reads several hundred bases away from each other. This ability is useful for analyzing SVs because paired reads can be aligned with the reference genome more accurately than single reads, and because we can analyze structures of genomes larger than the size of each read. However, SV detection is still a difficult task, because it requires analysis of the complex structures involved in an enormous number of alignments of paired reads with the reference genome, and because read sequences and alignments include unavoidable errors. Therefore, for example, a false detection rate (FDR) up to 10% had to be tolerated even when determining just the existence of each SV in the 1000 Genomes Project [2]. It is obviously more difficult to accurately detect the exact positions of SVs. Nevertheless, high-resolution SV calls are necessary to elucidate the functional impact of SVs and molecular mechanisms that generate SVs. Moreover, to conduct a large-scale analysis, SV detection methods for data with a low depth of coverage (hereafter simply referred to as coverage) are desirable, because whole genome sequencing is not easy even with NGS technologies.
Current methods for SV detection search for signatures that indicate SVs hidden in read sequences and their alignments with the genome sequences. The following are basic signatures used for SV detection [2-4].
• Read pair (RP) [5-7]: If pairs of reads have aberrant strands or distances, they are likely to be caused by SVs. Such pairs are called discordant pairs, and normally mapped ones are called concordant pairs. If strands of a discordant pair are as expected, a larger distance than expected indicates a deletion, whereas a smaller distance indicates an insertion. There are several categories of methods that detect discordant pairs by using mapping distances.
• Threshold-based: A pair with a mapped distance larger or smaller than a predefined threshold is defined as a discordant pair. The threshold is μ±3 σor μ±4 σfor BreakDancer [5] and VariationHunter [6] where μand σare mean and standard deviation of mapping distances, or median fragment size ± 10 median absolute deviations for HYDRA [7].
• Distribution-based: Although the mapped distance of a single pair might vary by tens or hundreds bases even without SVs, larger (smaller) mapping distances of many pairs in the same region indicate deletions (insertions). Such reads can be detected by statistical tests on the distribution of mapped distances [5,8]. Pairs detected in this way might have mapping distances more similar to the expected distance than those of other methods. Nonetheless, we still call them discordant pairs in this paper to unify the word used to refer pairs that support SVs.
• Graph-based: Recently Marshall et al. [9] proposed a new method CLEVER based on the graph theory. CLEVER constructs a graph where a node represents an alignment of a read pair and the genome, while an edge means that connected alignments potentially support the same allele. In this graph, a clique corresponds to a set of pairs supporting the same allele. CLEVER detects SVs by finding maximal cliques (max-cliques). CLEVER has an ability to find more than one max-clique overlaping each other, each of which supports a different allele. Therefore CLEVER can distinguish more than one SV located at the same locus, for example, two deletions of different sizes in a diploid genome.
• Read depth (RD) [10,11]: If coverage changes at some position in the genome, this indicates a copy number variation.
• Split read (SR) [12]: If an alignment of a read and the genome includes only a part of the read, this indicates a position of a breakpoint. Here, a breakpoint is the boundary between a region affected by some SV and its unaffected flanking region.
• Sequence assembly (AS) [7,13]: If the coverage is sufficient, assembling NGS reads around an SV reveals the exact sequence around the SV and the positions of breakpoints.
The most popular signature used to detect SVs is threshold-based RP. Methods based on this signature can detect SVs from a small number of discordant read pairs; therefore threshold-based RP methods can be applied to low-coverage data. However, threshold-based RP methods localize SVs only to regions surrounded by discordant read pairs, thus causing some ambiguity. For RD methods, the problem of resolution is much bigger. Because RD methods involve calculation of coverage in windows of a fixed size, its resolution cannot be finer than the window size. Methods based on the SR signature can determine positions of breakpoints up to base-pair-level (bp-level) resolution if there are reads covering the breakpoints. However, such reads might not exist, in particular when coverage is low, because of unevenness of coverage or repeat elements to which reads cannot be aligned uniquely. Moreover, because such a split alignment is shorter than a read itself, careful analysis is required to avoid spurious matches. If coverage is sufficiently high, AS methods would ultimately reveal the exact positions of SVs at bp-level resolution. Although extremely deep sequencing can be conducted by targeted sequencing [14], it is still expensive to obtain paired reads of high coverage over the entire genome so that assembly can be performed. In fact, a previous study has indicated that the sensitivity of AS methods is rather low (Table S6B of Mills et al. [3]).
Because these signatures have their own advantages and disadvantages, it is desirable to combine more than one method [4]. In fact, several methods that use more than one signature have been proposed recently [15,16]. In combined approaches, we should integrate SV signatures that are independent of each other. In this paper, we propose a new method called ChopSticks that improves the resolution of deletion calls for homozygous deletions generated mainly by threshold-based RP methods. ChopSticks is especially valuable when target SVs are expected to be homozygous as those of inbred mice whose genomes are homozygous at virtually all loci [17]. ChopSticks exploits positions of concordant read pairs in addition to those of discordant ones. Thus far, they have been ignored in threshold-based RP approaches, and therefore, our method can improve the resolution by using this new independent information. As explained below, ChopSticks is effective even for data whose coverage is low.
The organization of this paper is as follows. First, we theoretically analyze the improvement of the resolution achieved by exploiting concordant read pairs. Next, we present our computational method ChopSticks that improves the resolution of homozygous deletion calls. After that, we demonstrate the effectiveness of ChopSticks in computational experiments. Then, we present our conclusions. In addition, we illustrate details of our method and experiments in Methods section.
Results and discussion
Strategy for resolution improvement
Theoretical estimation of resolution
Here we present results of our theoretical analysis of improved resolution achieved by our method as compared to RP methods. We also present the necessary definitions to describe them. See Methods for details.
We define a discordant read as a read of a discordant pair and a concordant read as that of a concordant pair. Among the two reads of a pair, the one mapped upstream is called an upstream read and the other is called a downstream read in this paper. Let c be the depth of coverage. Assume that the positions of read pairs are uniformly random over the genome, and that the length r of each read is a fixed constant. Let q(c) be the probability that there is no read pair whose upstream read begins at a given base in the genome. Suppose that there are N read pairs uniquely mapped to a genomic sequence of length G. According to a classical analysis [18],
Hereafter, we just write q instead of q(c) for simplicity. In threshold-based RP approaches, the predicted position of an upstream end of a deletion is determined by the upstream discordant read that is the closest to the breakpoint. Let b be the position of an upstream end of a deletion, Δb be the distance between b and the closest upstream discordant read, and d be the distance between paired reads. We assume that d is a constant. Let E[Δb|b,c] be the expectation of Δbgiven that b is detected and the coverage is c. Then,
See Methods for derivation of Equation (2). We can obtain better resolution by using concordant reads in addition to discordant reads, because there is a chance that there exists a concordant read closer to b than any upstream discordant read (Figure 1). Such a read can contribute to the localization of the position where b can exist. Let be the distance between b and the closest read in the upstream of b, and let be the expectation of given that b is detected and the coverage is c. Then,
Figure 1. Resolution improvement by exploiting concordant read pairs. Schematic illustration of the key idea of our method ChopSticks. Unlike conventional SV detection methods based only on discordant pairs whose mapping distances were not close to the expectation, ChopSticks uses concordant read pairs as well. There is a chance that there is a concordant read closer to the boundary of the deleted region (breakpoint) than any discordant reads. Such a concordant read localizes the predicted position of the breakpoint, and therefore it contributes to achieving a high resolution. In this figure, b is the upstream end of a true deletion, Δb is the distance between the upstream end of a true deletion and that of a deletion call by threshold-based read-pair (RP) methods. Similarly, is defined for our method. The expected values of Δband are given by Equations (2) and (3), respectively.
As shown in Figure 2, the expected resolution of our method is significantly superior to that of threshold-based RP methods, which only use discordant pairs. The achieved resolution is quite close to that of threshold-based RP methods but with double coverage, which we confirmed theoretically.
Figure 2. Expected resolutions of ChopSticks and threshold-based RP methods. The expected resolution of our method () is shown by a thick red line, that of threshold-based RP methods (E[Δb|b,c]) is shown by a thin solid black line, and that of threshold-based RP methods with double coverage (E[Δb|b,2c]) is shown by a dashed black line. The difference between and E[Δb|b,2c] is also shown by a dotted blue line. As the coverage goes away from zero, the resolution obtained by our method quickly outperforms that of normal RP methods. It is also clear that the resolution of our method is very close to that of threshold-based RP methods with double coverage. The difference approaches zero when coverage approaches zero or infinity, as indicated by the blue dotted line. E[Δb|b,c], , and E[Δb|b,2c] are given by Equations (2), (3), and (5), respectively. In this figure, d=200 and r=100.
Theorem 1
The expectation is a weighted sum of E[Δb|b,2c] and E[Δb|b,c]. To be more precise, the following equation holds:
See Methods for the proof. When c→0, both E[Δb|b,2c] and E[Δb|b,c] approach d/2, which is the expected resolution when a deletion is detected with only one read pair. Therefore also approaches d/2 when c→0. On the other hand, when c approaches infinity, approaches E[Δb|b,2c] because qd + 1→0. In summary,
Theorem 2
is asymptotically equal to E[Δb|b,2c] when c→0 or c→∞.
Trimming of deletion calls to improve resolution
If all regions existing in the reference genome were covered by at least one read and there were absolutely no reads mapped to regions of homozygous deletions, the resolution of deletion calls could be quite easily improved by just trimming the ends of deletion calls that are covered by alignments of reads. Obviously, such a simple assumption does not hold in practical situations. First, coverage might be zero even in regions that actually exist in the genome, because no reads are obtained therein owing to the unevenness of the coverage or because reads cannot be uniquely mapped owing to repeat elements. Second, there might exist erroneous alignments in deleted regions because of incidental sequence similarity. Therefore, we developed the algorithm ChopSticks to carefully trim the ends of deletion calls (Figure 3). ChopSticks recognizes high-coverage regions close to the ends of deletion calls even if they are fragmented, and it repeatedly excludes the high-coverage regions from deletion calls. ChopSticks uses two parameters, k and f. The k parameter is a threshold used to distinguish high-coverage regions from low-coverage ones, and f determines the threshold of joint coverage of regions excluded from a deletion call. See Methods for details. Our implementation of ChopSticks is available on the Internet [19].
Figure 3. Overview of trimming algorithm of ChopSticks. Schematic illustration of the trimming algorithm of ChopSticks. ChopSticks trims ends of deletion calls that are not likely to be parts of deletions, according to their coverage. First, it trims high-coverage regions at the ends of deletion calls. Here, a high-coverage region is a region whose coverage is greater than a given parameter k. Second, it recognizes a high-coverage region separated by a low-coverage region and trims these regions if their joint coverage is deeper than kf, where f is another parameter. The second step is repeatedly conducted until the joint coverage becomes less than kf .
Computational experiment
To evaluate the power of ChopSticks in improving the resolution of deletion calls, we conducted computational experiments. Let the upstream difference of a deletion call be x−y, where x is the position of the upstream end of the true deletion and y be that of the deletion call. Similarly, let the downstream difference of a deletion call be y′−x′, where x′ is the position of the downstream end of the true deletion and y′is that of the deletion call. By definition, the closer to zero a difference is, the better. A positive difference value indicates that the called breakpoint is outside the true deletion, whereas a negative value indicates that it is inside the true deletion. To evaluate ChopSticks, the results of ChopSticks have to be compared with the positions of true deletions. Therefore we need NGS reads of a genome whose SVs against the reference genome are known up to bp-level resolution. We conducted two experiments described below.
Simulated reads
In the first experiment, we evaluated ChopSticks with simulated NGS reads for which all SVs were known up to bp-level resolution. To obtain data as realistic as possible, we generated a genome sequence with SVs and simulated NGS sequences by using SV annotations published by Quinlan et al. [7]. The accession number of the SV annotations is [dbVar:nstd19]. First, we deleted regions of the reference genome sequence that were annotated as deletions by Quinlan et al. Next, we inserted random fragments whose number and distribution of lengths were the same as annotated deletions, assuming that deletions and insertions are symmetric. Then, we introduced single nucleotide substitutions into the simulated genome sequence and generated paired reads from it. We conducted this simulation and evaluation of ChopSticks for chromosome 1 of the reference mouse genome mm9. All paired reads were mapped to mm9 using Burrows-Wheeler aligner (BWA) [20]. Then we conducted SV analysis by using SV detection tools from each of categories described in the Background section: BreakDancer [5] of threshold-based RP methods, MoDIL [8] of distribution-based RP methods, CLEVER [9] of graph-based RP methods, CNVnator [11] of RD methods, and Pindel [12] of SR methods. After that, we applied ChopSticks to their results.
Before applying ChopSticks, we examined the ability of SV detection tools to detect 460 deletions in chromosome 1 of the simulated mouse genome. We say that a deletion call is correct if it overlaps exactly one true deletion while the true deletion in turn overlaps exactly one deletion call. We show the number of called and correct SV calls in Table 1. We also show their recall (the number of correct deletion calls divided by the number of true deletions) and precision (the number of correct deletion calls divided by the number of all deletion calls) in Figure 4. The recall of BreakDancer and CLEVER was relatively good for all of tried coverage values, whereas the recall of Pindel was satisfactory only when coverage was high. The recall of MoDIL was low for all coverage values tried. Although almost all deletions called by these methods were correct, CNVnator generated numerous false positives (Table 1). Because ChopSticks is developed to correct breakpoints outside true deletions, we counted the number of deletion calls that cover the whole of true deletions. As shown in Figure 5, most of the deletion calls by MoDIL, CNVnator, and Pindel covered the whole of true deletions. However, a significant portion of BreakDancer and CLEVER results did not cover the whole of true deletions. Note that ChopSticks is harmless to these deletion calls because ChopSticks does not trim them when there are no alignments in true deletions.
Figure 4. Recall and precision of results of SV detection tools. BreakDancer and CLEVER achieved relatively good recall for all coverage, while recall of MoDIL was low. Although recall of CNVnator was not bad, its precision was low. The recall of an SR method Pindel was good when coverage was high, but it was insufficient when coverage was low.
Figure 5. Number of deletion calls covering the whole of true deletions. Solid lines and circles show the number of all deletion calls generated by each tool, whereas dashed lines and '+' symbol s show the number of deletion calls covering the whole of true deletions. Most of the deletion calls of MoDIL, CNVnator (expanded by the window size), and Pindel covered the whole of true deletions. On the other hand, many CLEVER results did not always contain the whole of true deletions, while median of the distribution of predicted breakpoints was close to the true breakpoints as shown in Figure 10. BreakDancer results for high coverage data did not always contain true deletions either. Predicted breakpoints of BreakDancer approached true breakpoints as the depth of coverage increases, and sometimes intruded into true deletions when coverage was high.
Table 1. Results of SV detection obtained by BreakDancer, MoDIL, CLEVER, CNVnator, and Pindel
Next, we applied ChopSticks to the results of SV detection tools. After that, we examined how well the resolution of deletion calls was improved. We tested ChopSticks for k=1,2,…,5 and f=0.1,0.2,…,1.0. We evaluated differences at both the upstream and downstream ends of deletions, and found that the results were similar. Therefore we only present the results at upstream ends.
Resolution improvements for BreakDancer deletion calls
As shown in Figure 6, the resolution of deletion calls was clearly improved by using ChopSticks. The original BreakDancer results was successfully corrected, which is also clear in Figure 7. When coverage was low, the resolution was well improved for small k values. When coverage was high, the resolution was also improved for large k values. Therefore, when the coverage is high, we recommend using large k values to ignore erroneous alignments. As shown in Figure 8, ChopSticks worked well regardless of deletion lengths.
Figure 6. BreakDancer results improved by ChopSticks. Box-and-whisker plots of upstream differences of deletion calls obtained by BreakDancer and those improved by ChopSticks. The red, green, blue, light blue, and magenta boxes correspond to k values of 1, 2, 3, 4, and 5, respectively, and the rightmost yellow box corresponds to the original results of BreakDancer. Among boxes of the same color, from left to right, f=0.1, 0.2, …, 1.0. Brown horizontal dashed lines indicate the values of 25%, 50%, and 75% tiles of differences of original deletion calls from below to above, respectively. The results in this figure indicate that ChopSticks clearly improved the resolution of the original BreakDancer results. When the coverage was low, small k values were effective in improving the resolution. When coverage was high, the resolution was also improved for large k values. Therefore, when the coverage is high, we recommend using large k values to avoid erroneous alignments of NGS reads and the genome. We omitted the results for coverage=15 because they were similar to those for coverage=20.
Figure 7. Distribution of differences of BreakDancer results and those improved by ChopSticks. The distribution of differences of ChopSticks results concentrated around zero, whereas that of BreakDancer results had long tail in 0–50 bp. Here, k=2, f=0.5, and coverage=5. Each frequency corresponds to the number of differences in bins of 2 bp.
Figure 8. Scatter plot of deletion lengths and differences of deletion calls. No correlation between deletion lengths and differences was observed (r2=0.056). ChopSticks worked well regardless of deletion lengths. Here, k=2, f=0.5, and coverage=5.
Resolution improvements for MoDIL deletion calls
As shown in Figure 9, the resolution of deletion calls by MoDIL was also improved by using ChopSticks. We omitted evaluation of MoDIL for coverage=20 because MoDIL was very slow (See Methods).
Figure 9. MoDIL results improved by ChopSticks. Box-and-whisker plots of upstream differences of deletion calls obtained by MoDIL and those improved by ChopSticks. The format of this plot is exactly the same as that in Figure 6, except that results for coverage=15 were shown instead of those for coverage=20. The results in this figure indicate that ChopSticks can also improve the resolution of MoDIL results.
Resolution improvements for CLEVER deletion calls
The resolution of deletion calls by CLEVER was also improved by using ChopSticks. As mentioned above, deletion calls of CLEVER do not always cover the whole of true deletions. Nonetheless, as shown in Figure 10 and 11, ChopSticks successfully improved resolution of CLEVER results by selectively correcting predicted breakpoints outside true deletions.
Figure 10. CLEVER results improved by ChopSticks. Box-and-whisker plots of upstream differences of deletion calls obtained by CLEVER and those improved by ChopSticks. The differences were successfully corrected. Note that a significant portion of breakpoints predicted by CLEVER were inside the true deletion. Nonetheless, ChopSticks selectively trimmed predicted breakpoints outside true deletions, and left those inside untouched.
Figure 11. Distribution of differences of CLEVER results and those improved by ChopSticks. The distribution of differences of CLEVER results had long tail in 0–50 bp, whereas that improved by ChopSticks concentrates around zero. Here, k=2, f=0.5, and coverage=5. Each frequency corresponds to the number of displacements in bins of 2 bp.
Resolution improvements for CNVnator deletion calls
Because RD methods call SVs by examining coverages in windows of a fixed size, the positions of breakpoints predicted by the RD methods have unavoidable ambiguity and they might be either inside or outside true deletions. Because ChopSticks assumes that predicted breakpoints are outside true deletions, we applied ChopSticks after we expanded deletion calls of CNVnator at both ends by the window size. As shown in Figure 12, the results of CNVnator were successfully improved. This result indicates that ChopSticks is also available for RD methods in addition to RP methods.
Figure 12. CNVnator results improved by ChopSticks. Box-and-whisker plots of upstream differences of deletion calls obtained by CNVnator and those improved by ChopSticks. The format of this plot is exactly the same as that in Figure 6. We expanded the original deletion calls of CNVnator outward by the window size (50 bp) because ChopSticks assumes that predicted breakpoints are outside true deletions. The results in this figure indicate that ChopSticks can improve the resolution of CNVnator results if predicted positions of breakpoints are within a few hundreds of bases from true breakpoints.
Results of ChopSticks applied to Pindel deletion calls
Owing to the SR signature that allows Pindel to detect SVs at bp-level resolution, the positions of breakpoints obtained with Pindel were quite accurate. When ChopSticks was applied to the results of Pindel, the results became slightly worse than the original Pindel results, as shown in Figure 13, although differences remained close to zero in most cases. Note that the recall of Pindel was not satisfactory when coverage is low, as shown in Figure 4. ChopSticks is useful in cases where deletions missed by Pindel are analyzed.
Figure 13. Pindel results and those modified by ChopSticks. Box-and-whisker plots of upstream differences of deletion calls obtained by Pindel and those modified by ChopSticks. The format of this plot is exactly the same as in Figure 6. The results in this figure indicate that ChopSticks should not be applied to the Pindel results because the resolution of the Pindel results is already quite high.
Real Illumina reads of DBA/2J
In the second experiment, we evaluated ChopSticks using the real NGS sequences of Quinlan et al. [7]. The sample was taken from a female mouse of the DBA/2J strain, whose genome contains SVs against the reference genome of the C57BL/6J strain [21]. The read sequences were available from the NCBI Sequence Read Archive (SRA) database [22]. The accession number of the read sequences is [SRA:SRA010027]. To evaluate the results of ChopSticks, we need bp-level SV annotations of DBA/2J as well. Therefore we generated deletion calls at bp-level resolution using Sanger reads in a manner similar to that of Quinlan et al. See Methods for details. Our deletion calls are available at the dbVar database under accession no. [dbVar:nstd70].
We tried the five SV detection tools used in the previous experiment, and found that MoDIL, CNVnator and Pindel missed the most of deletions detected with Sanger reads. These methods seemed to suffer from the low depth of coverage and short read lengths. Therefore, we hereafter only describe results of ChopSticks applied to BreakDancer and CLEVER results.
Resolution improvements for BreakDancer deletion calls
Figure 14 shows the differences between BreakDancer results and those improved by using ChopSticks. As the previous experiment where simulated NGS reads were used, the differences obtained with real NGS reads were reduced. The median and differences less than the median clearly shifted toward zero, which is also clear in Figure 15. Although ChopSticks trimmed some deletion calls into those based on Sanger reads when k=1 or k=2 and f was small, this problem quickly disappeared as k or f became larger. No correlation between deletion lengths and the performance of ChopSticks were observed (r2=0.021). Although we generated 525 deletion calls by using Sanger reads, only 83 of them were found by BreakDancer. There were at least two reasons for this difference in numbers. First, it is difficult to find small deletions because read pairs spanning small deletions might not be recognized as discordant pairs. Second, a lot of deletion calls based on Sanger reads had fewer than two NGS-read pairs spanning them. Such deletion calls would be missed because BreakDancer deletion calls must be supported by at least two pairs when the default parameters are used, in order to reduce false positives. For this data set, 82 of all 83 deletion calls generated by BreakDancer contained the whole of deletions predicted with Sanger reads.
Figure 14. BreakDancer results for DBA/2J reads improved by ChopSticks. Box-and-whisker plots of upstream and downstream differences of deletion calls obtained by BreakDancer and those improved by ChopSticks. The results in this figure indicate that ChopSticks can improve the resolution of deletion calls for real sequences. Although ChopSticks trimmed upstream ends of a few deletion calls too much when k=1 or k=2 and f was small, such problems quickly disappeared for greater k and f values.
Figure 15. Distribution of differences of BreakDancer results and those improved by ChopSticks. The distribution of differences of BreakDancer results had long tail in 0–400 bp, whereas that improved by ChopSticks concentrates around zero and frequencies in the long tail were reduced. Here, k=2, f=0.5. Each frequency corresponds to the number of differences in bins of 20 bp.
Resolution improvements for CLEVER deletion calls
CLEVER detected much more (347) deletions than BreakDancer. The results of CLEVER were also improved by ChopSticks as shown in Figure 16, where the peak around zero became stronger. However, it was difficult for ChopSticks to correct positions of breakpoints when they were away from those predicted with Sanger reads by hundreds of bases.
Figure 16. Distribution of differences of CLEVER results and those improved by ChopSticks. ChopSticks corrected some of breakpoints predicted by CLEVER so that the peak at zero became stronger. However, the distribution of differences of CLEVER results had long tail in 0–3000 bp and it was difficult for ChopSticks to correct such large differences. Here, k=2, f=0.5. Each frequency corresponds to the number of differences in bins of 20 bp.
We have presented a new method called ChopSticks to improve the resolution of predicted positions of deletions. The key idea is to exploit both concordant read pairs and discordant ones. According to our theoretical analysis, the resolution of our method is quite similar to that of threshold-based RP methods but with double coverage. In an experiment on simulated NGS reads, ChopSticks clearly improved the results of BreakDancer, MoDIL, CLEVER, and CNVnator. Although the resolution of Pindel results is quite high, ChopSticks works well even for low-coverage data where recall of Pindel is not sufficient. The effectiveness of ChopSticks was also confirmed by performing an experiment on real Illumina reads. Despite a number of methods proposed for detecting SVs [2-4], there is no one-stop method that simultaneously achieves high sensitivity, high specificity, high resolution, and robustness for low-coverage data. Therefore a combination of SV detection methods is required, and ChopSticks can play an important role because it uses new independent information ignored in other methods.
As a future work, we consider to develop a method to distinguish homozygous deletions from heterozygous ones and to apply ChopSticks to the former. With this approach, ChopSticks will be available for more applications.
Derivation of theoretical estimation of resolution
Because the resolution at downstream ends of deletions can be estimated symmetrically, we only analyze the resolution at upstream ends. Let Pbbe the probability that a breakpoint b is successfully included in a deletion call by a threshold-based RP method. If b is detected, there exists an upstream discordant read within d bases from b. Therefore,
We derive the expected distance between the true ends of deletions and the predicted ones in a manner similar to Bashir's analysis [23]. For 0≤j≤d, Bashir et al. defined Ajas an event in which b is detected and an upstream read of a discordant pair is exactly j bases upstream of b. The probability that Ajoccurs is
Similarly, we define as an event wherein b is detected and the closest read upstream of b is exactly j bases apart. There are two mutually exclusive cases: (i) at least one of the closest reads is an upstream discordant read or (ii) all the closest reads are concordant reads. In the latter case, we have to consider the joint probability of the following events.
• A concordant read exists at j bases upstream of b, the probability of which is 1−q.
• No read nearer than the closest concordant read exists, the probability of which is q2j.
• No discordant read exists at j bases upstream of b, the probability of which is q.
• There must exist an upstream read of discordant pairs whose alignment ends in a region that is j + 1 to d bases upstream of b so that b is successfully included in a deletion call, the probability of which is 1−qd−j.
Proof of Theorem 1
From Equation (1), E[Δb|b,2c] can be obtained by replacing qwith q2 in Equation (2):
From Equations (2), (3), and (5), Equation (4) can be obtained.
Proof of Theorem 2
First, we consider a case where c→0. Because q→1 by Equation (1),
Therefore, all of , E[Δb|b,2c], and E[Δb|b,c] approach d/2 by Equation (4). On the other hand, when c→∞, qd + 1approaches 0. In consequence, the right hand side of Equation (4) approaches E[Δb|b,2c] when c→0 or c→∞.
Mapping to the genome
We mapped paired reads to the mm9 reference genome sequences of Mus musculus using BWA version 0.5.9 [20] with default parameters. The target genome sequences involved in our experiment included all chromosomes of mm9 except chromosome Y, assuming cases where a female mouse was analyzed [7,21].
Simulated NGS sequences
To focus on uniquely mapped reads for BreakDancer, MoDIL, CLEVER, and ChopSticks, we removed paired reads if the mapping quality (MAPQ) score was zero for at least one of the two reads of a pair. For CNVnator and Pindel, we used the result of BWA without filtering. We show the total length of reads and the number of aligned reads in Table 2.
Table 2. Number of bases and number of reads of simulated data set
Real DBA/2J sequences
We split the data set of NGS reads into 275 subsets, and mapped each of them with an independent BWA process and merged the results. Then we removed reads whose MAPQ score was zero for at least one of the two reads of a pair. We show the total length of reads and the number of aligned reads in Table 3.
Table 3. Number of bases and number of reads of DBA/2J data set
Trimming algorithm of ChopSticks
The coverage outside a deletion should be higher than that inside it. Therefore ChopSticks repeatedly recognizes a high-coverage region in a deletion call that is likely a continuation of a high-coverage region outside the deletion. We show in Figure 17 the trimming algorithm executed by ChopSticks for upstream ends. Here is a brief description of the algorithm: Line 2: Skip a high-coverage region at the end of the deletion call. Lines 6–9: Go through a low-coverage region. Lines 10–13: Go through a high-coverage region. Line 14: If the joint coverage is low, exit the loop. Line 17: Trim regions which the algorithm has gone through.Trimming of the downstream ends is conducted symmetrically.
Figure 17. Pseudocode of trimming algorithm. Pseudocode of the trimming algorithm of ChopSticks. Here, L is the length of the deletion call being processed, k is a threshold used to discriminate high-coverage regions from low-coverage ones, and f is a parameter that determines the threshold of the coverage of regions to be trimmed. The variable x represents the position of the base being examined, and the variable y represents the length of a region to be trimmed. The value c[x] is the coverage at the x-th base in the deletion call, while s keeps the sum of c[x] values.
Data for computational experiments
To evaluate our method, we need NGS sequences and reliable bp-level positions of breakpoints. There were six SV studies of inbred mice (nstd5, 7, 15, 18, 19, and 48) in the dbVar database [22] when we accessed it on April 1, 2012. However, none of them provides accurate bp-level positions of breakpoints. Therefore, we evaluated ChopSticks using the following two data sets.
Simulated NGS reads
We artificially introduced deletions and insertions into the mm9 reference genome and then generated simulated NGS reads using the modified genome. To obtain most realistic simulated sequences, we built a simulated genome sequence using SV annotations generated by Quinlan et al. [7], which are available from the dbVar database under accession no. [dbVar:nstd19]. First, we deleted regions annotated as deletions in [dbVar:nstd19] from the mm9 reference genome sequence of chromosome 1. We show the distribution of lengths of deletions in Figure 18. Second, we inserted fragments consisting of randomly chosen bases so that the number and the distribution of lengths of inserted fragments were the same as those of deletions, assuming that the genome to be analyzed and the reference genome are affected symmetrically by deletions and insertions. Third, we introduced random single nucleotide substitutions with a probability of 1.0×10−4 at each base. Finally, we generated paired reads from the modified genome sequence so that the read length was 100 bp and the average and the standard deviation of distances of paired reads were 200 bp and 50 bp, respectively. We generated five sets of simulated NGS reads whose depth of coverage were 2, 5, 10, 15, and 20, respectively.
Figure 18. Distribution of deletion lengths in our simulation.
NGS reads of Quinlan et al. and deletion calls based on Sanger reads
We generated our own bp-level deletion calls by using publicly available Sanger reads of the DBA/2J strain. From the NCBI trace archive, we retrieved all 7,998,826 Sanger reads of whole-genome shotgun sequencing for the DBA/2J strain. We mapped these Sanger reads to chromosome 1 of mm9 by MegaBLAST [24], and we searched for Sanger reads that were split into two parts and aligned uniquely on the same strand and in the right order. There were 763 reads that indicated deletions whose lengths were at least 50 bp. By merging redundant ones, we obtained 525 deletion calls. These deletion calls are available in the dbVar database under accession no. [dbVar:nstd70]. We show the distribution of their lengths in Figure 19. NGS sequences of the DBA/2J strain generated by Quinlan et al. are available in the SRA database [22] under accession no. [SRA:SRA010027].
Figure 19. Distribution of deletion lengths detected with Sanger reads.
Parameters for SV detection tools and evaluation of their results
We executed BreakDancer with default parameters, and Pindel with an expected template size of 432 bp because the median fragment size was 432 bp according to Quinlan et al. [7]. For CNVnator, we tested three window sizes: 50 bp, 100 bp, and 200 bp. Because the recall of window size 50 bp outperformed those of window sizes 100 bp and 200 bp for our simulated data when coverage was 2, we used results of window size 50 bp for evaluation. Because CLEVER tends to generate deletion calls duplicatedly with slightly different positions, we chose the best one for those overlapping with true deletions in order to estimate the upper limit of the accuracy of CLEVER. We divided the chromosome 1 of mm9 into 5.1 Mbp fragments in a manner such that franking fragments share 0.1Mbp, and applied MoDIL to each fragments, because MoDIL was quite slow as reported previously [9]. We omitted evaluation of MoDIL for coverage=20.
To compare the positions of true and predicted deletions, we used BEDTools [25].
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
TY conceived the project, invented and implemented the algorithms, and performed the computational analysis. SS assisted TY in conducting experiments. MN and SM critically revised the manuscript. All authors read and approved the final manuscript
The super-computing resource was provided by Human Genome Center (University of Tokyo).
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