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Question: How to calculate differential methylated regions from MeDIP-seq data in Galaxy
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gravatar for RG
3.0 years ago by
RG • 0
RG • 0 wrote:

Hi all,

I am struggling to find a way to calculate DMRs from MeDIP-seq data in Galaxy. I know there are plenty R based program to do this, however since I am a total R-noob I will be limited to galaxy. 

We have 2 different seq samples from: control treated cells and cells treated with a cytokine. The idea is to know which regions in cytokine treated cells are enhanced related to the control cells.

I already acquired cytokine specific, control specific and overlapping regions using genomic overlaps. However as there is still a possibility that the overlapping regions are differentially methylated these will need to be calculated.

thanks in advance,

 

RG
dmr galaxy medip-seq • 1.2k views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by RG • 0
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Bismark is one tool for this type of analysis to consider. It is wrapped in the Tool Shed for use in a local or cloud Galaxy: https://toolshed.g2.bx.psu.edu/view/bgruening/bismark/0f8646f22b8d

There was a recent change to the output that permits it to be easier sent to SeqMonk (a stand-alone tool run on your computer) for more in-depth analysis/visualization. 

Peak calling is a bit different for this data type, but ChIP-seq tools might be used with some success (MACS, etc). Exploring some of the prior Q&A online at biostars, seqanswers, and others will give you an idea about what researchers are using. If you find a tool mentioned in a post or publication that you want to use in Galaxy, check the tool shed to see if it is already wrapped (many Bioconductor tools are, but not the package for this specific data as you noticed - but they could be). 

Others may have alternate opinions or advice. And you can request that tools be wrapped by the community here under "Issues": https://github.com/galaxyproject/tools-iuc

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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