I have 4 baits targeting the same locus, but at different adjacent RE fragments. I'm thinking I should just put one line in
.baitmap file (as well as the
.rmap file), like a big merged region. Is it right?
My second question is about
.chinput file. I'm going to convert the output wig file from https://github.com/Hughes-Genome-Group/captureC to
.chinput file. The question I have is that, for this wig file, read mapped wihtin +/- 1kb of the bait region are removed. Will it affect the CHiCAGO calculation?