Count splice junction reads from SAM/BAM files

Question

[juncheng]

Hi folks,

Is there any software available to count the splice junction reads for each junction? Specifically, I would like to count 1) exon-exon splicing reads, 2) exon-intron spanning reads for ALL JUNCTION SITES.

Considering alternative splicing events, I would also like to count exon-exon junction reads at each junction site for all exon-exon pairs.

I read on papers and see people do that, but I cann't come up with a easy way to do it. I would be good if anyone can suggest any software or ideas.

Best,
Jun

Answer 1

[Czh3]

plz try RNA-SeQC from broad.http://www.broadinstitute.org/cancer/cga/rna-seqc

this tools give you the number of reads mapping in exon/intron/intergene, and give you the number of junction reads.