Trying to reproduce a galaxy training in Linux CLI. I've come up with the following commands for the peak calling with MACS2. Am I on the right track? The galaxy parameters are-
macs2 command can be-
macs2 callpeak -t input_file.bed -n macs_output -g 50818468 --nomodel --shift -100 --extsize 200 --keep-dup all --broad-cutoff --call-summits --bdg
Is this okay to use 50818468 as effective genome size as I used only hg38 chromosome 22 as the reference genome in the alignment step? Thanks in Advance.