Question: Performing differential binding analyses between ChIP samples using Deeptools (SES method normalization)
0
gravatar for a.rex
9 months ago by
a.rex190
a.rex190 wrote:

I have 2 conditions under which I performed ChIP, each with 3 replicates. I want to perform differential binding analyses between them. I generally get a coverage file using the bamCoverage tool in deep tools (with the SES method) - this allows me to visualise my ChIP signal tracks and compare. But I really want to get a list of regions which are different; in the past peak calling methods have not been useful as the MACS peak calling for my samples tend to be wrong and I think it is because SES is more sensitive at look at enrichment over input.

Any ideas how I can avoid using MACS but still do this DiffBind type of analysis?

chip-seq • 340 views
ADD COMMENTlink modified 8 days ago by Jingyue30 • written 9 months ago by a.rex190
0
gravatar for Jingyue
8 days ago by
Jingyue30
United States
Jingyue30 wrote:

You can use Csaw (https://bioconductor.org/packages/release/bioc/vignettes/csaw/inst/doc/csaw.html) it use window-based method for differential binding analysis and can avoid using peaks from MACS2.

ADD COMMENTlink modified 8 days ago • written 8 days ago by Jingyue30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1398 users visited in the last hour