Extracting data from a .gff3 file

[jennaj]

Hi @kate2

I would suggest trying this!

First, convert your GFF3 to GTF format with gffread. Then, test to see if GTF2GeneList will extract the values you want pulled out from the attributes (9th column).

A tutorial has an example in this step (maybe what you used before!) → GTN Hands-on: Generating a single cell matrix using Alevin / Generating a single cell matrix using Alevin / Single Cell (generate-a-transcript-to-gene-map)

You likely know this already, but we have more manipulations in these tutorials!

@jennaj

• Hands-on: Data Manipulation Olympics / Data Manipulation Olympics / Introduction to Galaxy Analyses
• More → GTN Materials Search (query=olympics)

Please let us know how this goes or if you need more help!