Determine different methylation patterns after Bismark

cast457 · 10-09-2014, 01:41 AM

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!

dpryan · 10-09-2014, 02:14 AM

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.

cast457 · 10-09-2014, 02:33 AM

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?

dpryan · 10-10-2014, 11:21 AM

You'd have to code something to do that then, it's not something most people are interested in looking at.

cast457 · 10-11-2014, 05:08 AM

That's what I've expected. I am writing a perl script and will put in on github.

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10-09-2014, 01:41 AM	#1
cast457 Junior Member Location: Vienna Join Date: Sep 2014 Posts: 4	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!

10-09-2014, 02:14 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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.

10-09-2014, 02:33 AM	#3
cast457 Junior Member Location: Vienna Join Date: Sep 2014 Posts: 4	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?

10-10-2014, 11:21 AM	#4
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	You'd have to code something to do that then, it's not something most people are interested in looking at.

10-11-2014, 05:08 AM	#5
cast457 Junior Member Location: Vienna Join Date: Sep 2014 Posts: 4	That's what I've expected. I am writing a perl script and will put in on github.