Hi there!
I am running macs2 for peak calling of ChIP-seq data, but I don't know the effective genome size of UCSC hg38. Is anyone got a hint? The default value of macs2 is for hg18.
Thanks!
Hi there!
I am running macs2 for peak calling of ChIP-seq data, but I don't know the effective genome size of UCSC hg38. Is anyone got a hint? The default value of macs2 is for hg18.
Thanks!
Script to compute the effective genome size: epic-effective
Note that I get slightly different results than some papers, but no one on biostars seem to think my method for computing the egs is wrong.
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I'd just use the hg18 value though. I made my script for corn genomes etc, where the EGS is not known.