Count exon-exon junction reads for transcripts
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21 months ago
robinycfang ▴ 10

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

RNA-Seq STAR JUNCTIONS • 678 views
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Entering edit mode
21 months ago

bam2junc.sh script from leafcutter

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