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Old 06-23-2011, 01:37 PM   #3
Location: Bay Area

Join Date: Jan 2009
Posts: 58

Hi Jon

Thanks for your reply. The protocol is not standard we are trying to sequence the ends of transcripts using Mate Pair technique.

I data that I get after linker removal is of variable read length 60+/-20 bp. I reverse compliment the reads based on the basic definition reverse the read and then compliment it and also reverse the quality header.

One thing that could trick BWA is the variable fragment size as it dependent on the length of transcripts that we are trying to capture.

As per BWA options I have pretty much used the standard ones. At this point I am not so concerned about the mapping % as I am about the need for reverse complimenting the reads before mapping with BWA and how it handles the multi read mapping.

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