Identifying differential histone mark (H3k27me3 and H3k4me3) in treated and control sample

Question

[munaj86]

Hi,,

I'm analysing chip seq data for histone mark h3k27me3 and h3k4me3. for each condition, I have two samples: treated sample and control sample. I called the peaks for each sample using MACS2. Now, I want to compare between peaks file and identify the regions that have H3k27me3 in treated sample but not in the control and vice versa. So in general I want to perform differential histone modification between treated sample and control sample. Can anyone help me with that??

Thanks,,

[GouthamAtla]

If you don't have replicates, you can't do much with ChIPs. ChIPs are very heterogeneous that too for broad chromatin marks. If you have any plans to validate top peaks by ChIP-qPCR, you can use DESeq2.

Take the union of peaks from two replicates, quantify the reads using featureCounts and perform DESeq2 analysis.

[ATpoint]

Please read te vignette of csaw at Bioconductor for an introduction towards ChIP-seq differential analysis and normalization.