I have a large data set from an eCLIP experiment where the 5' end of my reads represents the nucleotide immediately after the crosslink sites between my protein of interest and the RNA it bound. I've seen that proteins usually crosslink to proteins at U's and I want to see if that's true in my data.
I would like to generate a heat map (or some sort of similar plot) that measures the frequency of each nucleotide 10-20 positions up and down stream of the 5' end of each of my reads from my bam files. Is there a program or script that can do this, or something similar?