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How find correlations between ChIP-seq tracks?

I have two ChIP-seq tracks - specifically H3K4me3 and H3K27me3. I have used DeepTools to calculate coverage of each of the marks around annotated TSS's.

How can I correlated between the two tracks at particular points around the TSS? i.e. I want an easy way to find genes that are represented at the TSS by both marks....

Cheers!

chip-seq analysis
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updated by Rashedul Islam Rashedul Islam • written by a.rex a.rex

4 answers

You can use deeptools' multiBamSummary/multiwigSummary with the BED-file sub command and then use plotCorrelation

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written by ejm32 ejm32

See if this script, localEnrichmentBed.py, is of any help. See also TPM for ChIP-seq normalization

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written by dariober dariober

Seqminer (https://sourceforge.net/projects/seqminer/) is old (2012), but allows you to download the genes from the different clusters you observe, something I have not managed to do with Deeptools.

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written by Ian Ian

From tracks, if it is wig or bigwig file, it is difficult to find whether "genes that are represented at the TSS by both marks".

If you have access to bam file, call the peaks and to intersect of the peaks to TSS.

To see the correlation, if you have bam file, count the number of mapped read around TSS and correlate.

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written by Rashedul Islam Rashedul Islam

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