MACS3 - custom genome

[PycnopodiaD]

Hi, I would like to use macs3 with a custom genome, or a genome that is not found on the list of the 4 genomes that can be used, is that possible? I tried using:

-g /path/to/the/genome/file.fa --2.5e9

But I just got an error message

macs3: error: unrecognized arguments: --2.5e9

If I leave that out I get;

ERROR:root:Available shortcuts of effective genome sizes are hs,mm,ce,dm

Maybe the syntax is just wrong? I don't know but it would be nice to be able to use another genome because I am not working on those 4 genomes.

[mrendleman]

The -g parameter just needs a number, not the path to your genome fasta. If your effective genome size is 2.5e9, use: -g 2.5e9

If you haven't calculated the effective genome size for your custom assembly, the documentation of deepTools has a nice overview and links to several tools you can use to calculate it.