I'm curious. What does the quality values data look like?
Is it continuous data, or ???
(if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
> I'm curious. What does the quality values data look like?
> Is it continuous data, or ???
>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>> > I'm curious. What does the quality values data look like?
>> > Is it continuous data, or ???
we would like them to be accessible in an efficient way. For example, when looking at alignments to a genome, the quality score is important to determine if you have a SNP or a problem with the aligned sequence.
>>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>>>> I'm curious. What does the quality values data look like?
>>>> Is it continuous data, or ???
an alternative to listing the space separated qual values would be to use the fastq method for storing that information, which essentially represents each qual value by its ASCII code (+32 I think to exclude the control characters). Then each qual value is one byte.
You could also encode those into a FASTQ quality string to condense them down if needed, but I would standardize them into the Sanger FASTQ format (please don't pick Illumina/Solexa variations!). All of the Bio* projects now have parsers that handle that conversion (I re-wrote the BioPerl one from scratch).
> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>> I'm curious. What does the quality values data look like?
>> Is it continuous data, or ???
scores for, and stash the actual phred scores in featureloc.residue_info.
too horribly ugly an implementation.
But maybe someone will have a better idea...?
>> we would like them to be accessible in an efficient way. For example, when looking at alignments to a genome, the quality score is important to determine if you have a SNP or a problem with the aligned sequence.
>> >>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>> >>>> I'm curious. What does the quality values data look like?
>> >>>> Is it continuous data, or ???
since the quality values are an important and a one-to-one property of the sequence, I was wondering if the easiest wouldn't be to just have an extra field in the table like 'qual' in addition to residues? It could be NULL.
> scores for, and stash the actual phred scores in featureloc.residue_info.
> too horribly ugly an implementation.
> But maybe someone will have a better idea...?
>>> we would like them to be accessible in an efficient way. For example, when looking at alignments to a genome, the quality score is important to determine if you have a SNP or a problem with the aligned sequence.
>>>>>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>>>>>>> I'm curious. What does the quality values data look like?
>>>>>>> Is it continuous data, or ???
consensus within GMOD for a schema change to a core chado table.
>> since the quality values are an important and a one-to-one property of the sequence, I was wondering if the easiest wouldn't be to just have an extra field in the table like 'qual' in addition to residues? It could be NULL.
>> > scores for, and stash the actual phred scores in featureloc.residue_info.
>> > too horribly ugly an implementation.
>> > But maybe someone will have a better idea...?
>> >>> we would like them to be accessible in an efficient way. For example, when looking at alignments to a genome, the quality score is important to determine if you have a SNP or a problem with the aligned sequence.
>> >>>>>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>> >>>>>>> I'm curious. What does the quality values data look like?
>> >>>>>>> Is it continuous data, or ???