[Bioc-sig-seq] qa from ShortRead

Martin Morgan mtmorgan at fhcrc.org
Tue Nov 2 17:29:58 CET 2010

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

Hope that helps. Martin

> -Kunbin
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