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Effective Genome Size for Masked MM9 36 bp reads
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2.3 years ago
landrjos • 10
@landrjos42728

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

ChIP-Seq genome • 204 views
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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

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