Effective genome sizes for peak calling

idonaldson

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Effective genome sizes for peak calling

02-25-2010, 05:09 AM

Apologies to anyone who also received this message via the MACS google group!

MACS requires the effective or mappable genome size for the reference genome used to map the NGS reads. What are people using for Drosophila melanogaster (DM3)?

I currently have this information for the following genomes:

Human (hg18) = 2700000000
- from MACS manual

Mouse (mm9) = 1865500000
- from MACS announcement (based on 70% of the whole genome size)

Yeast (sacCer?) = 12100000
- from MACS announcement

If anyone has this information for other genomes perhaps you would like to post them here?

Thanks,
Ian
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idonaldson

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02-26-2010, 06:41 AM

Thanks to Marco-Antonio MENDOZA-PARRA who replied to my MACS announcment posting:

"...I would recommend to use the table that has published in the Peak-seq paper where they estimate a mappable genome size of 121,40 Mbs (72% total genome) for Drosophila Melanogaster."

The paper in question can be found at PubMed: 19122651.

Drosophila (dm3?) = 121400000
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