Calculate correlations between ChipSeq data sets

Question

[Assa Yeroslaviz]

I am looking for a way to identify similarities between different ChIP-Seq data sets.

Is there a tool or an R package to calculate and/or plot correlations between different bedgraph (or bigWig) files from different ChIP-Seq runs (done with macs2) or homer.

thanks

[bernatgel]

If you want to test if the peaks are at the same regions, you can maybe try with regioneR. It won't test anything related to the shape of the peaks, though.

[Papyrus]

Also StereoGene to find correlations among many types of genomic feature data

[H.Hasani]

I would suggest deeptools

Answer 1

[Rory Stark]

The DiffBind package in Bioconductor will calculate correlation values and plot clustered correlation heatmaps (as well as PCA plots, which are are useful to assess similarity amongst ChIP-seq samples).

This works by looking at all the peaks (called by MACS2 in your case), forming a consensus set (default includes peaks overlapping in at least two samples), and calculating correlation values. You can get a more accurate view by also supplying the aligned reads (bam files) and re-counting the number of reads overlapping each condensus peak site in each sample (regardless of whether it was called as a peak in that sample).