GarrettJenkinson

Also while we are discussing the reference fasta, please ensure that it is sorted as discussed in the readme here: https://github.com/GarrettJenkinson/informME/blob/master/src/bash_src/parseBamFile/fastaToCpg/fastaToCpg_help.txt

You are correct that the tool is only expected to work for WGBS (so won't work in RRBS for example). What is the average depth of your "shallow" WGBS? In...

I do not have a docker and Matlab requires a license making it more challenging to dockerize. I suggest looking into the julia version here: https://github.com/GarrettJenkinson/InformMe.jl There are continuous integration...