Calculate correlations between ChipSeq data sets
1
0
Entering edit mode
2.3 years ago
Assa Yeroslaviz ★ 1.7k

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

chipseq correlation peaks bedgraph macs2 • 1.1k views
ADD COMMENT
1
Entering edit mode

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
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

I would suggest deeptools

ADD REPLY
0
Entering edit mode
2.3 years ago
Rory Stark ★ 1.5k

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

Login before adding your answer.

Traffic: 1287 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6