Codon counts from a bam file

Question

[sarthaks442]

How can I find codon counts from a bam alignment? I am still a newbie in next-gen sequencing analysis.

[Devon Ryan]

That's not something people normally want to do. Could you describe what your actual biological goals are? That would be helpful in guiding you.

[sarthaks442]

I am actually trying to analyse a codon translation rate model. I have a ribosome profiling dataset. I thought of counting using sam files by searching from a codon array. But that would take huge amount of time I think.