Two problems in download_genome_annotations when using old genome assemblies (with makeshift solutions) about scenicplus HOT 3 OPEN

Hi @franciskim-yonsei

Thank you for your detailed descriptions of your concerns, this is very helpful.
Indeed, modifying the biomart host is the correct way to get older assemblies. This could be better documented.

I was not aware of the url formatting issue!

The second problem you faced is very valid and this should not happen.

I have added this issue to my todo list!

Best,

Seppe

from scenicplus.

Can we also skip this error by specifying in advance the genome_annotation and chromsizes file paths in the output_data section of the snakemake config.yaml file (thereby avoiding running the download_genome_annotations rule of the Snakefile)?

from scenicplus.

Hi @davidhbrann

Yes, that's also a possibility!

All the best,

Seppe

from scenicplus.