XR-seq processing pipeline

Question

[sleepystudent]

Hi everyone! I want to re-analyze XR-seq data from this source and that source in order to check if there are some genes that are more damaged than others (due to the nucleotide content or anything else). However, as fas as I understand, there is no pipeline for doing it, because the mentioned data was analyzed for binding motifs.

I'd say from a scratch that the damage level for a particular gene should be the number of mapped reads, normalized by gene length and probably anything else. So I don't know if it is possible to apply some transcriptome-like analysis after alignment ? Any advices are appreciated.

Thanks!