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?
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
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.
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.
You can give MeQA a try