i Have few queries related to MeDip Seq Data analysis.
I have illumina MedipSeq data(Treatment sample R1,R2 and Normal Control data R1,R2). for which i have done initially mapping with bowtie2 and then used MACS for get peaks with scores then based on scores want to identify DMRs. so the question is, Is this the right way to do MedipSeq analysis. After Mapping the reads shall i remove duplicate reads ?, Is it great to just fetch only aligned mapped reads as bam file for DMR analysis.
I have read few papers like
- Methylome analysis using MeDIP-seq with low DNA concentrations
- Computational Analysis and Integration of MeDIP-seq Methylome Data
in these papers they have used MEDIPS, MeDUSA, BATMAN tools for MedSeq Analysis. is it better way to follow this protocol