Question: (Closed) Tools To Define Cis-Regulatory Modules And Associate Them To A Nearby Gene?
gravatar for Ahdf-Lell-Kocks
8.7 years ago by
Ahdf-Lell-Kocks1.6k wrote:

I would like to know of tools to define cis-regulatory modules for one or multiple TF ChIP-seq experiments that would take into account the inter-peak distance and the distance to the nearest gene at the same time when defining CRMs from the ChIP-seq dataset. What I've seen up until now are tools that first assign each peak to the nearest transcription start site and then define CRMs by setting a threshold for inter-peak distance within the peaks previously associated to a given TSS.

I would be interested in a tool that combines both distances, inter-peak distance and distance to upstream and downstream TSSs, at the same time.

binding chip-seq transcription • 1.9k views
ADD COMMENTlink modified 8.7 years ago by Casey Bergman18k • written 8.7 years ago by Ahdf-Lell-Kocks1.6k

This being a duplicate, I went to check the answers: am I right if I say that the first method with 3 perl scripts doesn't define CRMs for groups of peaks? And if one only has chip-seq data and no expression values, will then be essentially just associating peaks to nearest TSS based on distance? For the NAR paper in the second answer, I don't see a link to the code in the paper. Is this available somewhere or upon request to the authors?

ADD REPLYlink written 8.7 years ago by Ahdf-Lell-Kocks1.6k
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