Question: How find correlations between ChIP-seq tracks?
0
gravatar for a.rex
22 months ago by
a.rex220
a.rex220 wrote:

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 • 810 views
ADD COMMENTlink modified 22 months ago by Rashedul Islam370 • written 22 months ago by a.rex220
3
gravatar for ejm32
22 months ago by
ejm32440
Boston, MA
ejm32440 wrote:

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

ADD COMMENTlink written 22 months ago by ejm32440
1
gravatar for dariober
22 months ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

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

ADD COMMENTlink written 22 months ago by dariober11k
1
gravatar for Ian
22 months ago by
Ian5.6k
University of Manchester, UK
Ian5.6k wrote:

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.

ADD COMMENTlink written 22 months ago by Ian5.6k
1
gravatar for Rashedul Islam
22 months ago by
Canada
Rashedul Islam370 wrote:

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.

ADD COMMENTlink written 22 months ago by Rashedul Islam370
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