Question: motif for TF within CTCF boundary
gravatar for asharmatelome
5.1 years ago by
United States
asharmatelome60 wrote:


I want to find motif for my TF within the CTCF boundary. I have some 200 genes where I want to do this analysis. I was wondering if there is any tool to identify my TF binding motif within CTCF boundaries for all the genes in one go without doing it manually.



ctcf R genome • 1.3k views
ADD COMMENTlink modified 5.1 years ago by Alex Reynolds28k • written 5.1 years ago by asharmatelome60
gravatar for Alex Reynolds
5.1 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

FIMO will search for TF binding sites within your sequences of interest.

As input, you will need: 1) sequences of interest, and 2) PWMs for your TFs of interest (e.g., JASPAR, TRANSFAC, UniPROBE, etc.).

ADD COMMENTlink written 5.1 years ago by Alex Reynolds28k
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