Code reproducing the cCRE bed files

[gokceneraslan]

Hi,

First of all thank for this nice repo and the scripts reproducing the results. We have been using the bed files for CREs in the brain CATlas work (http://catlas.org/catlas_downloads/humanbrain/cCREs/cCREs.collapse.bed and http://catlas.org/catlas_downloads/humanbrain/cCREs/cCREs.bed) as a comprehensive list of all brain CREs. I was wondering whether the scripts producing that file are here in this repo, especially how they are merged, mapped to bins and how you come up with this particular robust set of CREs.

[yal054]

Hi, thank you for your interests!

I put the scripts I used under folder "bin" of this repo. you can find more detailed descriptions from this link:
https://github.com/yal054/snATACutils/tree/master/03.peak_calling

for the peak calling processing, it includs serveral steps. I hope you can find more details in the Methods and Extended Data Fig. 15 from my previous work: https://www.nature.com/articles/s41586-021-03604-1#Sec9

Please let me know how i can help further.