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Old 01-17-2011, 06:05 AM   #1
Location: Singapore

Join Date: Oct 2009
Posts: 44
Default Counting reads that jump over a position

Dear all,

I would like to count reads that are present before a feature and after a feature, but not in the feature. My Input is a *.bam file and the features are exon described in .gtf format.

I would like to count the PE reads (and their mates) that map before an exon and after it (exclusion reads), but not in it. This is neccessay to calculate the inclusion ratio of exons.

Is there a way to do this with BedTools?

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