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Old 05-24-2012, 04:32 AM   #22
EGrassi
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Location: Turin, Italy

Join Date: Oct 2010
Posts: 66
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I see, thanks. I did this evaluation with picard (and separately with awk on the bam file, should be similar to your perl) but with alignments done on the transcriptome because it seemed the sensible thing to do to me...maybe I was utterly wrong...ASAP I will perform some tests and report back here.

(the $idist formula could be cleaned removing some -1/+1 I believe , as in $second_mate->start - $first_mate->end -1)
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