Tools To Define Cis-Regulatory Modules And Associate Them To A Nearby Gene?
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.
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Casey Bergman
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Ahdf-Lell-Kocks •
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Ahdf-Lell-Kocks •
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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?