Monday, 4 July 2011

BWA SOLiD Paired Ends mapping

The short answer seems to be 'no' BWA can't do it yet.
(I went through steps like the one here to find that out in the end, the only difference is that I used a modified to process the F5 correctly)
   bwa sampe
expects the orientation to be the same as SOLiD mate pair
while reverse complementing the F5 might work, that itself is problematic due to the colorspace nature of SOLiD reads.

Your options?
Bioscope :(
or bowtie (if you don't need indels) see

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Datanami, Woe be me