Thread: subread
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Old 06-01-2013, 11:20 PM   #3
Jon_Keats
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Location: Phoenix, AZ

Join Date: Mar 2010
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For subjunc analysis I'm a bit confused by the following parameters:

-d --mindist <int> the minimum distance between two reads in a pair, 50 by default
-D --maxdist <int> the maximum distance between two reads in a pair, 600 by default

If you have fragments of 150 bp which are sequenced with 100x100 HiSeq runs then you have read1 covering from 1-100 and read2 covering 50-150. So would the --mindist be -50?
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