Hello!
I am using pysamstats to calculate the number of mismatches, deletions and insertions per base in my RNAseq data. The RNA was treated with a chemical such that sites which are single stranded end up getting mutated, deleted etc. However, I am running into a problem as pysamstats is counting spliced regions as deletions. Does anyone know of a way I could fix this problem? Maybe a way I could get pysamstats to only consider deletions smaller than 4bp? Or some other program that could give me this information in a tab format?
Thanks!
I am using pysamstats to calculate the number of mismatches, deletions and insertions per base in my RNAseq data. The RNA was treated with a chemical such that sites which are single stranded end up getting mutated, deleted etc. However, I am running into a problem as pysamstats is counting spliced regions as deletions. Does anyone know of a way I could fix this problem? Maybe a way I could get pysamstats to only consider deletions smaller than 4bp? Or some other program that could give me this information in a tab format?
Thanks!
Comment