What is the correct way to get the total number of reads strictly contained in each interval in a GFF from a BAM file while enforcing strandedness? What I am looking for is very close to this intersectBed
feature:
-c For each entry in A, report the number of overlaps with B.
- Reports 0 for A entries that have no overlap with B.
- Overlaps restricted by -f and -r.
Except that I'd like the number of overlaps in A for each entry in B (i.e. the other way around). If I do:
intersectBed -abam mybam.bam -b mygff.gff -s -f 1 -wb
Then my understanding is that this will report the entry in B for each overlap with A. But I'd like each entry in B to be outputted exactly once, with the number of reads from A that are contained strictly within it. I'm not sure how to enforce strict containment here.
Is coverageBed
the solution to this? Or multicov
? I'm not sure how to enforce strict containment using coverageBed
- it's not clear to me if that's the default from the docs. Thanks.