I am brand new to ChIP seq and this type of analysis! Very excited to learn but unfortunately currently at a roadblock.
I have .BED files after peak calling with MACS, and unfortunately don't have access to any upstream alignment/BAM files. I have 62 files total, from 62 different samples. I have been trying to use HOMER to count reads, and eventually create a count matrix, but I'm stuck on making Tag directories. It states that it requires alignment files, which I don't have, so not sure how to proceed.
I also looked at using bedtools "multicov", but this looks like it requires BAM files as well. I can't seem to make any progress to figure out what to do next, so any help would be truly appreciated. Many thanks.