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Old 01-22-2015, 11:38 PM   #2
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Location: Berlin, Germany

Join Date: Jan 2015
Posts: 137

You can extract the overlapping coverage data with bedtools intersect, e.g.

bedtools intersect -wb -a coverage.bdg -b transcripts.bed
(-wb is helpful to see which transcript in the "b" file overlapped the features in the "a" file - you could add transcript identifiers to the "b" for easier parsing)

But if you are actually interested in the actual number of reads overlapping with transcript features, you're probably better of using the original BAM with a GFF3/GTF file and HTSeq-count ( - it has some further interesting features for RNA-Seq (if that's what you're into).
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