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 [email protected] and delete this message, along with any attachments, from your computer. > > _______________________________________________ Bioc-sig-sequencing > mailing list [email protected] > 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
