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Old 05-02-2011, 07:32 PM   #1
Location: Stanford, CA

Join Date: Feb 2010
Posts: 12
Default Using trimmed reads in bwa (PE100bp data)

Hi All,

Bioinformatics newbie here, so excuse me if I ask a dumb question (to which the answer could not be found in the bwa manual).

I generated paired-end 100bp reads from genomic DNA, and trying to align to hg19 using bwa. I converted my raw reads from illumina-fastq into sanger-fastq already.

Then, I have used an external script to trim my reads based on quality (specifically, DynamicTrim of the SolexaQA package), and now want to proceed to the bwa alignment. Before I go to bwa aln, I want to ask, if after trimming a particular read becomes very short, shorter than the bwa seed length, then how does bwa deal with this particular read? And since my data is paired-end, does it also treat the other mate pair the same way? (e.g. if the way it deals with reads shorter than seed is to discard them, then does it also discard the corresponding mate pair?)

BWA has been giving me a lot of trouble, and the manual isn't much help for troubleshooting, so I appreciate any insight from this forum.

Thank you!

Last edited by angelawu; 05-02-2011 at 07:37 PM.
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