Question: Identifying novel ChIP-seq peaks in KO samples compared to WT
1
gravatar for jotan
3.8 years ago by
jotan1.2k
Australia
jotan1.2k wrote:

I have two ChIP-seq tracks of a histone modification from WT and KO cells which have been processed in parallel. I also have input tracks for both samples. The histone modification is diffuse across the genome and does not form clear peaks. Peak calling is therefore very difficult. Normally, to identify novel binding sites, I would call peaks on WT and KO samples individually and then intersect the two peak files.

In this case, I am considering calling peaks on the KO sample using the WT sample as my "input" to identify novel regions of enrichment.

Both the ChIP samples and the matched inputs are similar to each other with comparable read counts.

Are there any reasons why this would be a bad idea?

 

 

chip-seq • 1.6k views
ADD COMMENTlink modified 3.7 years ago by vanvanka60 • written 3.8 years ago by jotan1.2k
1
gravatar for Sean Davis
3.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Just one of many options, but you might take a look at csaw:

https://bioconductor.org/packages/release/bioc/html/csaw.html

ADD COMMENTlink written 3.8 years ago by Sean Davis25k

Thanks for that. I'll have a look.

ADD REPLYlink written 3.8 years ago by jotan1.2k
1
gravatar for vanvanka
3.7 years ago by
vanvanka60
RWTH Aachen University Hospital
vanvanka60 wrote:

If you have replicates try out THOR

www.regulatory-genomics.org/THOR

or ODIN if you don't have replicates

www.regulatory-genomics.org/ODIN 

both methods handle input DNA. 

ADD COMMENTlink written 3.7 years ago by vanvanka60
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