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rajanil / msCentipede

A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
MIT License
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Using TRAP to obtain motif files #13

Closed antgomo closed 8 years ago

antgomo commented 8 years ago

I'm a new msCentipede, and I am planning to do TF foot printing analysis using on ATACseq paired-end data.

My main concern is that I want to see if there is TF binding on my data, but first I want to look for all TFs, i.e all PWMs on JASPAR, so I am planning to use TRAP because is fast to doing this. DO you thinks is appropiate to do it?

rajanil commented 8 years ago

I haven't used TRAP myself. However, if the output of TRAP is a list of motif sites that a TF likely would bind to, then these sites would be an appropriate input to msCentipede.

I've observed msCentipede to be fairly robust to the set of motif sites used for learning, as long as the set includes many potential binding sites (typically, sites with high PWM scores). So, any software (TRAP, FIMO, others ...) should suffice.

antgomo commented 8 years ago

OK, many thanks Anil!