Counting Spliced Pair-End Reads

Question

[Frenkiboy]

Is there an application that can count the number of overlaps between a BED/GTF file and splice mapped pair-end reads?

(e.g. interval 1 in bed is overlapped by 10 fragments)

Thanks!

Answer 1

[Mikael Huss]

Yes, BEDTools among others. You can use intersectBed and give it a BAM file with alignments (which can be spliced and paired-end) and a BED/GTF file with intervals.

Answer 2

[Botond Sipos]

Check out also the htseq-count tool shipped with the HTSeq Python package.