Question: Calculate correlations between ChipSeq data sets
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gravatar for Assa Yeroslaviz
12 months ago by
Assa Yeroslaviz1.4k
Munich
Assa Yeroslaviz1.4k 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

ADD COMMENTlink modified 12 months ago by Rory Stark920 • written 12 months ago by Assa Yeroslaviz1.4k
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 REPLYlink written 12 months ago by bernatgel2.9k

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

ADD REPLYlink written 12 months ago by Papyrus690

I would suggest deeptools

ADD REPLYlink written 12 months ago by H.Hasani980
0
gravatar for Rory Stark
12 months ago by
Rory Stark920
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark920 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 COMMENTlink written 12 months ago by Rory Stark920
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