Question: tools for alignment and methylation extraction for MeDIP sequencing
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gravatar for ruchi19sinha
12 months ago by
ruchi19sinha0 wrote:

For methylation study in cancer, we have MeDIP-seq data. What are all tools that we can use for alignment and calling methylation. Can Bismark be used for the same?

chip-seq alignment next-gen • 225 views
ADD COMMENTlink modified 12 months ago by ATpoint40k • written 12 months ago by ruchi19sinha0

Alignment can be done with standard tools. It is plain DNA-seq as no bisulfite conversion was done. You do not need Bismark. Analysis could be done with MEDIPS in R/BioC: https://bioconductor.org/packages/release/bioc/html/MEDIPS.html

ADD REPLYlink modified 12 months ago • written 12 months ago by ATpoint40k

Thanx for your reply... Actually once i had tried Bismark tool for MeDIP alignment and methylation extraction. As as result, I have identified true methylated side. This I have confirmed after checking each position in Integrative Genomics Viewer (IGV) with respect to reference genome. I am surprised how I'm getting correct result, if bismark does not work for meDIP-seq.

ADD REPLYlink modified 12 months ago • written 12 months ago by ruchi19sinha0

I am no expert in methylation analysis but the idea of Bismark is that it deals with reads that were bisulfite-treated so you would need to align against an in-silico bisulfite-converted genome and then make calls on the CpGs that have been protected by methylation from the conversion. MeDIP is using antibodies against methylated Cs without any conversions. From my understanding you simply align this like any normal ChIP-seq experiment.

ADD REPLYlink written 12 months ago by ATpoint40k

Hi ruchi19sinha

You can give MeQA a try

ADD REPLYlink written 12 months ago by lakhujanivijay5.3k
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