text: hi,
  how I could know whether my data sets coming from RNA-seq are strand-specific or not????? I emailed the company but they are in Chinese new year and could not help me yet but I should start the analysis.
  thank you
  hi,
  how I could know whether my data sets coming from RNA-seq are strand-specific or not????? I emailed the company but they are in Chinese new year and could not help me yet but I should start the analysis.
  thank you
  Align a million or so reads (using the unstranded mode, if your aligner has one) and then use RSeQC to infer the experiment type.
  Just to complete your suggestion with a link =)
  thank you, then I need both bam and bed files? but in UCSC Table Browser there is no such a bed for Arabidopsis, then what to do?
  Get the bed from BioMart (Ensembl plant):
  Make sure the genome build matches.
  thank you, for aligning I used gtf coming from ensembl but there is gff3. no problem???
  the main problem is this, I tried to convert my gtf to bed by bedops but some bug that I could not solve then I tried galaxy but in galaxy there is only gff to bed then I used my gtf instead of gff but
  [izadi@lbox161 bin]$ infer_experiment.py -r Galaxy142-[GFF-to-BED_on_data_141].bed -i 204.bam
  infer_experiment.py: No match.
  [izadi@lbox161 bin]$
  then do you know another solution please?
  ./infer_experiment.py -r Galaxy142-[GFF-to-BED_on_data_141].bed -i 204.bam
  Looks like you need to provide the path for infer_experiment.py since that does not seem to be in that bin directory.
  thank you but please consider
  [izadi@lbox161 bin]$ pwd
  /usr/data/nfs6/izadi/RSeQC-2.6.3/usr/bin
  [izadi@lbox161 bin]$ ls
  204.bam junction_saturation.py
  bam2fq.py mismatch_profile.py
  bam2wig.py normalize_bigwig.py
  bam_stat.py overlay_bigwig.py
  clipping_profile.py read_distribution.py
  deletion_profile.py read_duplication.py
  divide_bam.py read_GC.py
  FPKM_count.py read_hexamer.py
  Galaxy142-[GFF-to-BED_on_data_141].bed read_NVC.py
  geneBody_coverage2.py read_quality.py
  geneBody_coverage.py RNA_fragment_size.py
  infer_experiment.py RPKM_saturation.py
  inner_distance.py split_bam.py
  insertion_profile.py split_paired_bam.py
  junction_annotation.py tin.py
  [izadi@lbox161 bin]$
  Try this in case Devon's suggestion did not work
  $ python ./infer_experiment.py -r Galaxy142-[GFF-to-BED_on_data_141].bed -i 204.bam
  thank you,
  [izadi@lbox161 bin]$ python infer_experiment.py -r Galaxy142-[GFF-to-BED_on_data_141].bed -i 204.bam
  python: No match.
  [izadi@lbox161 bin]$
  :(
  You don't have python installed on this machine? What OS are you using?
  $ which python
  fedora22
  [izadi@lbox161 bin]$ which python
  /bin/python
  [izadi@lbox161 bin]$
  Looks like python/infer_experiment.py does not like that atrocious BED file name. Can you move/copy it to something else and try.
  $ cp Galaxy142-[GFF-to-BED_on_data_141].bed simple.bed $ ./infer_experiment.py -r simple.bed -i 204.bam
  thank you,
  [izadi@lbox161 bin]$ infer_experiment.py -r simple.bed -i 204.bam
  Traceback (most recent call last):
  File "infer_experiment.py", line 49, in <module>
  from bx.bitset import *
  ImportError: No module named bx.bitset
  [izadi@lbox161 bin]$
  thank you
  [izadi@lbox161 RSeQC-2.6.3]$ python setup.py build
  running build
  running build_py
  running build_ext
  running build_scripts
  [izadi@lbox161 RSeQC-2.6.3]$
  [izadi@lbox161 RSeQC-2.6.3]$ sudo python setup.py install
  [sudo] password for izadi:
  Sorry, user izadi is not allowed to execute '/bin/python setup.py install' as root on lbox161.mpikg.mpg.de.
  [izadi@lbox161 RSeQC-2.6.3]$
  You could ask your sys admins to install the modules or try to install them in your own directory:
  It is a bit late in this thread but can't you ask whoever produced this data if they used a "strand-specific" protocol?
  thank you
  I emailed the company but they are in holliday
  Not ideal but you could look at the alignments in IGV/Tablet to see if you can see an identifiable pattern in the alignment of reads.
  thank you so much
  in a biostars post I read something about sam flags
  then i saw
  abundances of 83, 99, 147 and 163 flags of my sam file is the same=1 , then might library IS sequenced strand-specific
  anyway I think they will back from holiday Feb 14 and may they reply my email
  sorry, I installed Python then this is my result
  Reading reference gene model simple.bed ... Done
  This is PairEnd Data
  Fraction of reads failed to determine: 0.0068
  Fraction of reads explained by "1++,1--,2+-,2-+": 0.4992
  Fraction of reads explained by "1+-,1-+,2++,2--": 0.4940
  my library was sequenced in strand-specific mode? sorry if so first or second strand?
  thank you
  No it was not strand-specific. See the explanation here:
  Eeek, I had a few missing words in there too! Thanks for adding the link!