[Bioc-sig-seq] qa from ShortRead

[Martin Morgan]

On 11/02/2010 09:08 AM, Kunbin Qu wrote:
> Hi, all:
> 
> I have a question about the qa function in ShortRead. I have some
> fastq sequences with an offset of 33 to encode the quality scores.
> As far as I understand Illumina's encoding uses an offset of 64. The
> quality score vs cycle plot generated from the "qa" seems a little
> low. Is there a way to adjust the offset in qa? Thanks.

Hi Kunbin --

please start a new thread rather than reply'ing to an existing post and
changing the subject line.

please provide the output of sessionInfo() in all posts.

please include a short example of the code you are using, preferably
executable (e.g., based on example(qa) or example(readFastq)).

fastq files do not encode quality score, so as documented on ?readFastq
there is an argument qualityType that determines how the quality scores
are interpreted.  Use qualityType="FastqQuality" in readFastq. If you
invoke qa() with type="fastq", then add qualityType="FastqQuality" as an
argument.

Hope that helps. Martin


> 
> -Kunbin
> 
> 
> 
> ______________________________________________________________________
>
> 
The contents of this electronic message, including any attachments, are
intended only for the use of the individual or entity to which they are
addressed and may contain confidential information. If you are not the
intended recipient, you are hereby notified that any use, dissemination,
distribution, or copying of this message or any attachment is strictly
prohibited. If you have received this transmission in error, please send
an e-mail to postmaster at genomichealth.com and delete this message, along
with any attachments, from your computer.
> 
> _______________________________________________ Bioc-sig-sequencing
> mailing list Bioc-sig-sequencing at r-project.org 
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793