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Question: How to count novel and known splice junction reads from BAM
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gravatar for Anil Kesarwani
5.7 years ago by
Anil Kesarwani • 90
United States
Anil Kesarwani • 90 wrote:

Hi,

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
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modified 5.7 years ago by Jordan • 1.2k • written 5.7 years ago by Anil Kesarwani • 90
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gravatar for Jordan
5.7 years ago by
Jordan • 1.2k
Pittsburgh
Jordan • 1.2k 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

 

 
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