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Old 10-09-2014, 01:41 AM   #1
cast457
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Default Determine different methylation patterns after Bismark

Hi Guys,

I have a bismark sam-file including 66 different targets. The next step will be to detect different subpopulations for all targets in terms of the CpG island - considering only the reads with a coverage of e.g. 80%. I am not interested in the statistics of every single CpG position. Since I have not found any tool for that, I wonder how I can do this step efficiently. What would be your approach?

Cheers!
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Old 10-09-2014, 02:14 AM   #2
dpryan
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It's really unclear what you're actually trying to do. You say you're not interested in individual CpGs, which implies that you'd like to look at regions. Are the 66 different target different samples or did you perform targeted bisulfite sequencing? In the case of the latter, how big are the regions and would you like to just summarise methylation over them? If not, you'll need to provide more details on what you'd actually like to do.
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Old 10-09-2014, 02:33 AM   #3
cast457
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Sorry for being unclear. Well I have 66 different regions of interest. And so far I found serveral tools that gave me proportions of every single CpG (methylated - unmethylated) or show me fully methylated regions like CellMethy. However, I wanna see, which subpopulations are found in each region. Lets say we have a region with 4 CpGs. What patterns can be found in that region? X-x-x-x? Or also x-X-x-x?
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Old 10-10-2014, 11:21 AM   #4
dpryan
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You'd have to code something to do that then, it's not something most people are interested in looking at.
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Old 10-11-2014, 05:08 AM   #5
cast457
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That's what I've expected. I am writing a perl script and will put in on github.
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