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Old 04-09-2012, 08:53 AM   #1
okyoon
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Location: Berkeley, CA

Join Date: Sep 2008
Posts: 3
Default bowtie2 read length in score-min

I am trying to use bowtie2 in local mode to allow soft-clipping.
The parameter "score-min" lets me define a read-length dependent function for the threshold score.
My question is whether "read length" refers to the full length or the soft-clipped length.
If the CIGAR says 40M10S, is the read length 50 or 40?
Thank you.
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