Question: Count splice junction reads from SAM/BAM files
0
gravatar for juncheng
4.7 years ago by
juncheng190
köln
juncheng190 wrote:

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

splice junction rna-seq • 3.2k views
ADD COMMENTlink modified 4.7 years ago by Czh3190 • written 4.7 years ago by juncheng190
1
gravatar for Czh3
4.7 years ago by
Czh3190
China
Czh3190 wrote:

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.

ADD COMMENTlink written 4.7 years ago by Czh3190
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