[BioC] girafe issues - no interval overlap

[karlerhard at berkeley.edu]

Hi list,

I've identified what I think is a problem in my girafe analysis: I am
getting ZERO overlaps between my aligned read intervals (from BAM file)
and my annotation intervals from the interval_overlap function used in the
girafe package.

I'm pretty sure that the BAM file is ok, it inputs fine and is recognized
as an "AlignedGenomeIntervals" object using class(my_bamfile). Although
I'm using a subset of my dataset for troubleshooting, I've checked (with
my own eyes) and there are definitely intervals in this list that do
overlap with intervals from my gff file.

So I suspect there is some formatting issue with my gff file, but I'm not
sure what it is.

I'll keep searching, but if anyone has an idea as to what could be causing
this discrepancy, it would be super.

karl

Grad Student - UC Berkeley