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