I'm working on a chip-seq experiment in Wheat, which has a very large and repeptitive genome.
I'm a bit baffled by the "effective genome size" parameter in macs2. I understand it is related to the repetitiveness of the genome but I'm not sure how to calculate it. I've tried GEM but it gave me an error, so in parallel to trying to solve the GEM problem, maybe someone has an alternative?
Secondly, if I'm looking for peaks in repeptitive as well as non-repetitve regions of the genome, I thought maybe I should use the full length rather than the mappable length. Am I correct?
Finally - if I have a control sample (no antibody), can that be used to estimate the mappability of the genome?