Count exon-exon junction reads for transcripts

Question

[robinycfang]

Dear all,

I downloaded some bam files from TCGA, and I am hoping to count the exon-exon junction (intronic) reads for each transcript, so basically something like SJ.out.tab produced by STAR. I believe the TCGA bam files were mapped by STAR, but I couldn't find SJ.out.tab files. Is there a way to count the junction reads without remapping data with STAR? Any suggestions on the tools? Thanks!

R

Answer 1

[GouthamAtla]

bam2junc.sh script from leafcutter