Effective genome size for MACS2 in allele specific Chip-Seq
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13 months ago
liang795 • 0

Hello,

I am using MACS2 to call peaks for allele specific Chip-seq result. However, I am not sure how I should set the effective genome size for it. Since I used SNPs to distinct different allele-mapping, the effective genome size for G1 and G2 should be different, but should I use the effective genome size estimated from the whole genome or I should use a different genome size for different alleles? If so, may I know how I should calculate that? Thank you so much!

ChIP-Seq macs2 genome size • 346 views
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