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Question: Calculate correlations between ChipSeq data sets
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gravatar for Assa Yeroslaviz
12 months ago by
Assa Yeroslaviz • 1.4k
Munich
Assa Yeroslaviz • 1.4k wrote:

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
bedgraph correlation macs2 chipseq peaks • 484 views
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modified 12 months ago by Rory Stark • 920 • written 12 months ago by Assa Yeroslaviz • 1.4k
1

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.

ADD REPLY • link written 12 months ago by bernatgel • 2.9k

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

ADD REPLY • link written 12 months ago by Papyrus • 690

I would suggest deeptools

ADD REPLY • link written 12 months ago by H.Hasani • 980
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gravatar for Rory Stark
12 months ago by
Rory Stark • 920
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark • 920 wrote:

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). enter image description here
ADD COMMENT • link written 12 months ago by Rory Stark • 920
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