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Old 02-04-2016, 12:28 PM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
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Perhaps I am missing something here but if (a) you have a mapping and (b) know which reads are from prey-only then you should be to -- via samtools view, cut, grep, sort, uniq and the rest of the Linux tools -- generate a count of prey-only, prey+target, target-only for each transcript.

I am not sure if SAMtools per se would help.
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