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Old 06-26-2013, 07:26 AM   #1
jazz
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Location: us

Join Date: Nov 2008
Posts: 28
Default compare genomic features from gff file to a SAM/BED file

I have an alignment from Bowtie2 for my RNA-IP and I want to compile a pie chart of % of reads mapping to different genomic features like exons, introns, UTR's etc. I am planning to compare my BAM/BED file to a genome annotation gff file. I have heard of intersectbed in bedtools, however the gff files and bed files have genomic coordinates in different columns. can anyone suggest a simple fix for that? I have also heard of people using mpileup option in samtools, although I have no idea how that would work here. I am a bioinformatics newbie, so writing custom scripts is out of question at this point. Given that this is a very commonly sought after problem, I am hopeful that one of the great minds would have found an easy solution for this.
Thanks in advance!
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