For paired-end RNA-seq data I've been using featureCounts (subRead suite) because it produces a nice output, treats paired reads as a single fragment for counting, and accepts a very simple annotation file format that is easy to make.
However, when I tried to use it just now to count reads aligned to a draft genome that has more than 10,000+ scaffolds (blueberry) it crashed with a segmentation fault.
Rather than dig through the code to find out what's wrong, I'm taking a second look at htseq-count.
Does anyone know if htseq-count can accept bed files? The documentation doesn't say anything about BED files - just GFF. I found a post on BioStars somewhere that said it could take BED, but the documentation doesn't mention it.
I really, really don't want to have to convert my annotations file into GFF because GFF is so open to interpretation.
All I want is the number of fragments that overlap a set of spans on my genome. For my application, I know the general region of every gene but the fine details of where exons and introns start and end are still up in the air. Which means: I just need to know the number of fragments that map onto simple intervals that are defined by contig name, start, and end position.