Any thoughts any one. What does Y and N mean in the case of a read pass of fail filter?
On 8/19/14, 4:26 PM, Alec Wysoker wrote: > Hi Ogan, > > Could you please send your reply to the whole list so that other > members of my group see it? > > Thanks, Alec > > > On 8/19/14, 4:20 PM, Abaan, Ogan (NIH/NCI) [E] wrote: >> Thank you Alex for the prompt reply. It may very well be but, here is >> the follow up. I am running rnaseqc on these files, and it labels >> majority of the reads failed filter as well. That is what got look >> into all of this to begin with. >> >> Are we really sure that Y is meant pass filter, check this out too >> http://seqanswers.com/forums/showthread.php?t=19891 >> >> I have a feeling "N" was meant for passed filter >> >> Ogan >> >> >> On 8/19/14, 3:50 PM, Alec Wysoker wrote: >>> Hi Ogan, >>> >>> I believe the wikipedia article is not very clear. Y means passed >>> filter. At least that is what IlluminaBasecallsToFastq intends it >>> to mean. >>> >>> -Alec >>> >>> On 8/19/14, 3:41 PM, Abaan, Ogan (NIH/NCI) [E] wrote: >>>> I have tried the most current version of picard as well, but seem to >>>> have the same issue. When I run IlluminaBasecallstoFastq, with >>>> read-format as casava_1_8, I get nice fastq files with proper headers, >>>> but, almost all of the reads are labelled "Y" for pass-filter >>>> failed or >>>> not. I see from the QC metrics that most of the reads passed >>>> filter, so >>>> why picard is labeling them as failed filter. I think "Y" stands for >>>> failed filter and "N" stands for not failed filter, at least thats >>>> what >>>> it says here http://en.wikipedia.org/wiki/FASTQ_format "Y if the >>>> read is >>>> filtered, N otherwise" >>>> >>>> Can anybody help me out to sort the problem? >>>> >>>> Thanks >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> >>>> _______________________________________________ >>>> Samtools-help mailing list >>>> Samtools-help@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/samtools-help >>> >> > ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
