a script to calculate the regulatory potential

[crazyhottommy]

Hi Allen,

This is Tommy. I was trying to connect with you on Linkedin :) I know you rewrote Lisa and you have some script built-in to calculate the regulatory potential score (RP).

Given a bed file (peaks), a bigwig (intensity) and a gene model (e.g., gtf) file, I need to calculate the RP for every gene based on ATACseq data, do you have a script for that? I trust your implementation and do not want to re-invent the wheel.

Thanks! Hope all is well with you PhD at Harvard!

Tommy

[qinqian]

Hi Tommy,

Here is my previous implementation of the regulatory potential score (https://github.com/qinqian/histonerp), it implemented the function you want here for ATAC-seq and histone modification ChIP-seq data. You could directly use the docker file to build the image, let me know if you have any question @crazyhottommy .

Best,
Alvin

[crazyhottommy]

Thanks @qinqian ! Let me open an issue on your repo.