Wrong counts for BAMPairedFragmentCollection over regions read in from a bed file

[pamelarussell]

I wrote a program to get counts over intervals and they are totally wrong. Also, strandedness/unstrandedness of annotation doesn't change the count at all, which it should as the fragments are stranded. Specifically, I'm creating a BAMPairedFragmentCollection and getting counts over regions read in from a bed file.

[charcuterie]

I don't know how you're constructing these intervals, but if you're reading them in from a paired-end BAM file, keep in mind that this issue could be related to #1. (I discovered #1 when my counts didn't make physical sense.)

[pamelarussell]

I'm reading the intervals in from a bed file. They're just simple intervals like chr3 1000000 2000000. I don't think it's related to #1, in which you saw lower counts than expected. I see counts around 3,000-4,000 for a wide variety of intervals; they should not all be in this range, and when I look in IGV, many of them only have a few reads mapped to them. It's almost as if there are ~3,000 fragments that cover the entire chromosome or something.