readBins with M, GC and N score for all chromosomes

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julie dubois

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May 21, 2013, 6:51:38 AM5/21/13
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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

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May 21, 2013, 10:01:32 AM5/21/13
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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

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May 21, 2013, 10:55:36 AM5/21/13
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Ok, Thanks a lot for your proposition! I'm using a bin size of 200 bp.

Thanks.
Julie

Dongjun Chung

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May 23, 2013, 12:17:02 AM5/23/13
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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:
Thanks,
Dongjun


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julie dubois

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May 29, 2013, 4:09:26 AM5/29/13
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Thanks!
It's perfect.


Julie

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

Aayushi Jain

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Feb 12, 2016, 9:55:00 PM2/12/16
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Hi Dongjun!

Can you please make these files available again?

Thanks
Aayushi
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Dongjun Chung

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Feb 12, 2016, 11:46:35 PM2/12/16
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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:
Best,
Dongjun


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Aayushi Jain

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Feb 13, 2016, 2:45:47 PM2/13/16
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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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