tools for alignment and methylation extraction for MeDIP sequencing

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4.5 years ago

ruchi19sinha • 0

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 next-gen alignment • 837 views

ADD COMMENT • link updated 4.5 years ago by ATpoint 82k • written 4.5 years ago by ruchi19sinha • 0

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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 REPLY • link 4.5 years ago by ATpoint 82k

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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 REPLY • link 4.5 years ago by ruchi19sinha • 0

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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.