Human hg38 GTF, source Gencode

Hi @jennaj - I’ve been reading through these threads as I have had the same problem - thank you for your wisdom so far! Please could I just confirm what you mean by “Avoid the gff3 version”?

Because when I click on GENCODE’s human GTF files I see they are all gff3 files. I am confused which one I need to choose (I have included a screengrab below):

  • For context I am running RNA STAR on Galaxy for Illumina paired-end reads of human pancreatic cancer cells that I want to align to the human hg38 genome

Hi @mariannebest

The column with the “Download” links include both formats. Copy the link for the GTF, paste that into the Upload tool, and leave all “auto” settings at default.

The datatype will be detected as “GFF”.

Two additional steps are need to format this data correctly:

  1. Remove the # header lines, #working-with-gff-gft-gtf2-gff3-reference-annotation
  2. Then redetect the datatype, #detecting-the-datatype-file-format

This should result in the datatype set as “GFT” and the tools you are using will understand how to use this annotation with any (most?) other data that use or incorporate data also associated with the hg38 genome assembly.

Hope that helps!

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Thanks so much!! :smiley:

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