I am on paleogenomic data. I have BAM files from two different datasets that were processed/sequenced different (one was partially UDG treated, one was not UDG treated at all - the latter was sequenced on a newer machine).
Most of my comparisons between the two datasets are plagued by batch effects. One idea my adviser asked me to try is clip the first 5-10 bp off all reads within all BAM files. The problem is neither of us know how to do that.
Anyone here know of a way to trim reads within a BAM file?