Effective Genome Size for Masked MM9 36 bp reads

Question

[landrjos]

Hi All,

I was wondering if anyone knows the effective genome size for the masked MM9 build using 36 bp reads with 1 mismatch? Do I need to determine this with software? If so how would I do it. I need this number to do a GC correction of my ChIP-Seq data.

Best,

Joe

[landrjos]

Hi All,

A common effective genome size used for the unmasked MM9 genome is 2,150,570,000. Would masking reduce this to 58% because 58% of the genome is non repetitive. Is it that simple?

Joe