Genome annotation (gtf/gff3) from GenCode or Encode?

[LarionovBioinformatics]

Ask away!

In your GitHub instructions ( https://github.com/epi2me-labs/wf-transcriptomes ) you wrote that for the ref_annotation file "A reference annotation in GFF2 or GFF3 format (extensions .gtf(.gz), .gff(.gz), .gff3(.gz)). Only annotation files from Encode, Ensembl and NCBI are supported." Could it be a type: Encode instead of the GenCode ( https://www.gencodegenes.org/ ). If this is not a typo, could you also support resources from GenCode: this is a very popular source for human and mouse.

[sarahjeeeze]

Hi, thanks for the suggestion. We will update it to mention gencode. It has certainly been tested with gencode files so should work - let me know if any problems. I thought as gencode is part of encode it would make sense to call it encode but I see gencode makes more sense.