Counting reads per codon

Question

[fire_water]

Hello. So I have some ribosome profiling sequencing data which I've clipped, trimmed, mapped with Bowtie, and converted to BAM files for viewing in IGV. The data looks good in IGV but now I want to know the number of reads per codon. Does a tool exist for doing that?

Thanks!

Answer 1

[Jorge Amigo]

none that I'm aware of, but codon information can be considered as any other annotation, so if you have all the codons you're interested in described in a bed file you can obtain such information using bedtools intersect for instance:

bedtools intersect -c -a codons.bed -b reads.bam