I guess the quality of the data does not change however the downstream qc tools
flag this that is how it came to my attention. The current code has a command
line option for read name format whether its the old illumina read names or the
new casava1-8. And this flag only is output in casava mode, therefore its
critical to make it match what it was supposed to do. If nobody really output
casava, which does not really have any benefit, they will be spared from this
issue.
Ogan
-----Original Message-----
From: "Lee Edsall" <leds...@ucsd.edu>
Sent: 8/19/2014 5:44 PM
To: "Nils Homer" <nho...@broadinstitute.org>; "Abaan, Ogan (NIH/NCI) [E]"
<aba...@gmail.com>
Cc: "samtools help" <Samtools-help@lists.sourceforge.net>
Subject: Re: [Samtools-help] picard IlluminaBasecallstoFastq
The pass-filter flag changed in casava 1.8 so that might be where some of the
confusion comes from. Previous versions used "Y" if the read passed the
Chastity filter and "N" if it didn't.
A couple of options come to mind:
1. Add a command line parameter to indicate if the files are casava version 1.8
(or later)
2. Use the quality score encoding to determine if the files are from casava
version 1.8 (or later). In casava 1.8 the quality score encoding changed to
phred+33 (to match what the rest of the world has been doing for years).
Previous versions used phred+64.
Hope this helps!
Lee
Received from Nils Homer on 8/19/14 5:11 PM:
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] <aba...@gmail.com>
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
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Samtools-help mailing list
>>>> Samtools-help@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>>
>>
>
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