Codons from rna seq bam file?

Question

[protprot]

I am trying to identify codons from certain regions of interest in my bam files. Are there any tools to do this?

[h.mon]

Is the reference a genome or transcriptome? Is the reference annotated? By "identify codons from certain regions", you mean you want to infer the most likely codon from the reads?

Can you provide a more concrete example?

Answer 1

[Eric Lim]

Not sure if there's a tool that would turn bed into codons or amino acids. If you were to do this yourself, bedtools getfasta (https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html) is one of the many ways to turn coordinates into sequences. Unless you're translating in all 6 frames, you'll need strand and reading frame. Both can be found in columns 7 and 8 of a gff file. Also, be aware of 0- or 1-based coordinates to make sure you're not off by 1. One last thing. If your coordinates contain spliced junctions, you'd need to parse and get only coding sequences, which could quickly complicate the process. This isn't likely a trivial exercise for someone who is very new to python, or programming in general.