using MACS2 with hg38

Question

[varsha619]

Hi! I am wondering if there has been any updates regarding using MACS2 with hg38. I have my files aligned to hg38 and used genome option in MACS2 as default for 'hs' which I am not sure is still hg18 or if it has been updated to hg38. Please let me know, thank you!

Answer 1

[igor]

The -g/--gsize parameter in MACS is "the mappable genome size or effective genome size which is defined as the genome size which can be sequenced". It's not really the actual reference sequence. The mappable genome size has not changed much (especially as it applies to short reads). Even if you assume it changed significantly, there are still big differences between different variants of hg38.

[varsha619]

Hi Igor, thank you for your reply. Do you think it's ok for the files to be aligned to hg38 and MACS2 run with the -g/--gsize parameter?