I am trying to follow a pipeline from a paper that compares two sam files and generates a new file based on the minimum coverage value of the two. To make things clearer here is what the paper says:
“For sample A and sample B, reads were aligned separately, and per-base coverage was normalized to 10M reads. For each base pair, true coverage was defined as the minimum coverage of sample A and sample B.”
I know about bamCompare and bamCoverage from deeptools but while they can do the normalization, they can’t take the minimum of the two files.
Any ideas how I can do this?
Edit: I found that we can do this with WiggleTools. Also made some edits because I had previously misinterpreted what the paper did and I cant delete the thread.