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Old 01-10-2012, 06:59 AM   #4
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Location: Kansas City

Join Date: Mar 2008
Posts: 197

I think you could use genomeCoverageBed from bedtools for the first step. I know you could do the second part in R quite easily, but it would take me awhile to figure that one out. Once you have a bed file you could use intersectBed to get a bam just with those coords.
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