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Old 01-04-2013, 04:30 AM   #1
Jluis
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Location: Bilbao

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Default How to classify promoters according to CpG density

Hello everybody,

A research collaborator has asked us to classify promoters according to their CpG density. Data comes from a RRBS (Reduced Representation Bisulfite Sequencing) analysis in mouse (using mm9 sequence as template) and I don't have a clue on how to do this.

-Any of you knows about any tool, script or R-package that allows to do this ?
-Is there any repository where I can download a BED file where this kind of information is already available for organisms different than human?

We've been reading different papers that present such data but I haven't been able to understand how they manage to obtain such classification and then represent it graphically.

Any insight would be appreciated.

Thanks in advance.

JL

PD. I've been given this set of conditions. I write them here just in case anybody (even the authors of some similar analysis) may recognize an analog issue reading them, so that they can suggest a tool, script or R package that perform this calculation:

"To determine promoter classes, we measured the GC content and the CpG ratio of observed to expected values in sliding 500-bp windows with a 5-bp offset in regions -900 bp to +400 bp relative to the TSS. Promoter classes were defined as follows: LCPs contain no 500-bp window with a CpG ratio >0.45; HCPs contain at least one 500-bp window with a CpG ratio >0.65 and GC content >55%; ICPs do not meet the previous criteria."

Last edited by Jluis; 01-04-2013 at 05:34 AM.
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Old 01-06-2013, 04:33 PM   #2
frozenlyse
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The Bioconductor package Repitools has a function cpgDensityCalc which will run on any BSgenome organism available on Bioc, and whichever gene annotations you supply.
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Old 01-07-2013, 12:28 AM   #3
Jluis
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Thank you frozenlyse, I'll take a look at it and see if it works in my particular analysis.

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