readBins with M, GC and N score for all chromosomes

[julie dubois]

Hi,
It's a trivial ask, but I want to run the command readBins on my chip sample with input and GC, mappability and N score.
I use the mm9 genome, I've downloaded your pre-processed files which are mm9_GC.txt for each chromosome separately and also mm9_map and mm9_N files.
For example : How can I process readBins(type=c("chip","M"),fileName=c("mySampleOnAllChromosomes","????")...) when I have 22 files for the type "M" ?

Must I process this command on each chromosome separatly ?! Or how can I make one file for all chromosomes in a good format for this command ?

Thanks.
Julie

[Dongjun Chung]

HI Julie,

Those files are for chromosome-wise analysis using ChIP filles obtain by byChr=TRUE in constructBins().

In your case, you need to feed genome-wide version M, GC, and N files for mm9 to readBins() and we can provide these files for you (we already have these files for many genomes but we just could not put them to the website yet) as well. Which bin size are you using? If you let me know, I can put the files you need in our public space.

Thanks,
Dongjun

[julie dubois]

Ok, Thanks a lot for your proposition! I'm using a bin size of 200 bp.

Thanks.
Julie

[Dongjun Chung]

Hi Julie,

I generated genome-wide version of mappability, GC content, & N files for mm9 of bin size 200 and put them to the following place:

https://www.dropbox.com/sh/rt2s3bv3b9mfto0/j1hZfOQXHu/mm9

Thanks,
Dongjun

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[julie dubois]

Thanks!
It's perfect.

Julie

On Tuesday, May 21, 2013 12:51:38 PM UTC+2, julie dubois wrote:

[Aayushi Jain]

Hi Dongjun!

Can you please make these files available again?

Thanks

Aayushi

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[Dongjun Chung]

Hi Aayushi,

We actually constructed and maintained a FTP site dedicated to the storage of M, GC, and N files for various organisms. Please check the following link and let me know whether it works for you:

ftp://ftp.cs.wisc.edu/pub/users/kelesgroup/MOSAiCS/

Best,

Dongjun

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[Aayushi Jain]

Thanks again !

-Aayushi

Aayushi Jain

B.Tech, M.Tech (Biochemical Engg), IIT Delhi

Graduate Student, Lewis Lab

Integrated Program in Biochemistry

University of Wisconsin-Madison

Madison, 53706

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