Effective Genome Size Of Mm10 For Macs14

Has anyone already figured out the effective or mappable genome size of mm10 to be used with Macs as an input argument.

-g GSIZE, --gsize=GSIZE Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs

Thanks

macs chip-seq

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updated 4.5 years ago by Ram

• written 13.8 years ago by Sukhi Singh

Any reason you don't want to use the mm9 value? I can't imagine it's that different, and if their method is that sensitive to this parameter, you probably won't be too happy anyways...

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written 13.8 years ago by matted

Yeah, I think the results wouldn't be effected that much, still just thought someone have already done the exercise calculating it :)

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written 13.8 years ago by Sukhi Singh

I'm going to try this tool GEM for a different genome, you could try it. https://groups.google.com/forum/#!topic/macs-announcement/-iIDkVwenn8

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updated 4.5 years ago by Ram

• written 11.7 years ago by Madelaine Gogol

1 answer

let's see:

> wget http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit
--2012-10-19 09:44:43--  http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit
Resolving hgdownload.cse.ucsc.edu... 128.114.119.163
Connecting to hgdownload.cse.ucsc.edu|128.114.119.163|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 714784109 (682M) [text/plain]
Saving to: `mm10.2bit'

100%[==========================================================>] 714,784,109 1.61M/s   in 7m 59s  

2012-10-19 09:52:42 (1.42 MB/s) - `mm10.2bit' saved [714784109/714784109]
> twoBitToFa mm10.2bit stdout | grep -v ">" | perl -lane 's/[^ACGTacgt]//g; $sum += length $_; print $sum if ($sum > 2e9)'
[few thousands lines omitted]
2652783500

so 2.65e9 is your answer.

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written 13.8 years ago by JC

Hi, I think its not true in context with Macs14 of what they call as effective genome size. See this It's the mappable genome size or effective genome size which is defined as the genome size which can be sequenced. Because of the

repetitive features on the chromsomes, the actual mappable genome size will be smaller than the original size, about 90% or 70% of the genome size. The default hs — 2.7e9 is recommended for UCSC human hg18 assembly. Here are all precompiled parameters for effective genome size

So, I would assume it to be little more or less than the 1.87e9, what they estimated for mm9 by removing the repetitive region. A similar post : http://biostars.org/post/show/19380/

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written 13.8 years ago by Sukhi Singh

true, my number is the efective genome size, I don't know if Macs14 apply a special filter. BTW hg18 efective size is 2,881,421,696.

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written 13.8 years ago by JC

Down rated - sorry. But in relation to this question and MACS the answer is wrong. Refer to Sukhdeep's comment.

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written 13.8 years ago by Ian

I accepted I was wrong ..., I up voted Sukhdeep's comment

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written 13.8 years ago by JC