Using MACS2 parameters
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10 months ago
Nishat • 0

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- Galaxy Parameters

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.

linux galaxy bedgraph peak_calling macs2 • 308 views
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