Question: How to count novel and known splice junction reads from BAM
gravatar for Anil Kesarwani
5.7 years ago by
United States
Anil Kesarwani90 wrote:


I have BAM file from TopHat 2 alignment with RefSeq genes annotation. Is there any way to count separately the exon junction reads comming from RefSeq transcripts and novel junctions (not from RefSeq).

Could somebody help me out.

rna-seq tool • 2.3k views
ADD COMMENTlink modified 5.7 years ago by Jordan1.2k • written 5.7 years ago by Anil Kesarwani90
gravatar for Jordan
5.7 years ago by
Jordan1.2k wrote:

I have never tried this. But may be you can use bamtobed tool to convert the regions in bam to bed format. And then find common regions between this bed file and the gtf file.

You can may be try the following steps.

Step1: Convert bam to bed
bedtools bamtobed -i reads.bam > reads.bed

Step2: Convert gtf to bed
gtf2bed < refseq.gtf > refseq.bed

Step3: Compare the common regions between the two bed files
bedops --everything reads.bed refseq.bed



ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by Jordan1.2k
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