Hey Abaan,
it looks like your interpretation is correct for the Casava 1.8 read name
structure, namely that "Y" means that the read has been filtered, "N"
otherwise [1]. The current Picard software outputs "Y" if the read has not
been filtered, namely it has passed filtered, "N" otherwise. Given that
this software has been in use for a while, we have to consider how we move
forward with this issue, though the change in the code should be trivial.
Thanks for reporting this,
N
[1]
http://supportres.illumina.com/documents/documentation/software_documentation/bcl2fastq/bcl2fastq_letterbooklet_15038058brpmi.pdf
On Tue, Aug 19, 2014 at 4:32 PM, Abaan, Ogan (NIH/NCI) [E] <[email protected]
> wrote:
> 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
> >>>>
> >>>>
> ------------------------------------------------------------------------------
> >>>>
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> >>>> [email protected]
> >>>> https://lists.sourceforge.net/lists/listinfo/samtools-help
> >>>
> >>
> >
>
>
>
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