Has anyone used BWA for mate pair reads? We've had some trouble on first effort. Appears it's mapping the inward facing reads but not handling the outward facing reads (the true jumps). Any advice? Is it necessary to invert reads first?
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BWA does not support jumping libraries. Nonetheless, you may consider to switch read1 and read2 (putting read2 as the first file and read1 as the second). I have not tried though.
EDIT: I was right. Forget my claim. BWA does not support jumping libraries. Please use another aligner.Last edited by lh3; 03-30-2010, 05:30 AM.
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