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tools for alignment and methylation extraction for MeDIP sequencing

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
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updated by ATpoint ATpoint • written by ruchi19sinha • ruchi19sinha

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.

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written by ruchi19sinha • ruchi19sinha

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.

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written by ATpoint ATpoint

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