Question: How find correlations between ChIP-seq tracks?
0
gravatar for a.rex
6 months ago by
a.rex170
a.rex170 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 • 363 views
ADD COMMENTlink modified 6 months ago by Rashedul Islam290 • written 6 months ago by a.rex170
3
gravatar for ejm32
6 months ago by
ejm32430
Boston, MA
ejm32430 wrote:

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

ADD COMMENTlink written 6 months ago by ejm32430
1
gravatar for dariober
6 months ago by
dariober9.9k
Glasgow - UK
dariober9.9k wrote:

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

ADD COMMENTlink written 6 months ago by dariober9.9k
1
gravatar for Ian
6 months ago by
Ian5.3k
University of Manchester, UK
Ian5.3k 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 6 months ago by Ian5.3k
1
gravatar for Rashedul Islam
6 months ago by
Canada
Rashedul Islam290 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 6 months ago by Rashedul Islam290
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