search

chung-lab / SCAFE

Single Cell Analysis of Five'Ends
MIT License
43 stars 11 forks source link

using 10X references #22

Open ktpolanski opened 1 year ago

ktpolanski commented 1 year ago

Hello,

I'm interested in using the tool, and would ideally be able to use the same reference genome as what was used for the cellranger mapping (e.g. GRCh38-2020-A). However, it seems that only the GTF and fasta are present as part of the reference. The chromosome list should be trivial to generate, but how would I go about obtaining the BED? A cursory googling of ENCODE CRE did not turn up anything promising.

Thanks a lot and sorry for the trouble.

ktpolanski commented 1 year ago

This question becomes quite a bit less pressing upon realising that GRCh38-2020-A is built from gencode v32, which seems to be line up quite nicely with hg38.gencode_v32. Nevertheless, it would still be nice to find out how to get the BED, if you have a moment at some point.

yxsee commented 1 year ago

I downloaded the human cCREs from https://screen.encodeproject.org/ under the downloads tab. Hope this helps