Counting Spliced Pair-End Reads
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!
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Botond Sipos
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Frenkiboy
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Frenkiboy
2 answers
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.
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Mikael Huss
Check out also the htseq-count tool shipped with the HTSeq Python package.
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