Request to add Sus Scrofa species compatability with AnnotatemyIDs and EGSEA

[rlynn01]

I would like to use AnnotatemyIDs and EGSEA to visualize the pathway enrichment for my significant genes. Is there a way to add compatibility with the Sus Scrofa species? Thank you in advance!

[jennaj]

Hi @rlynn01

Only a few species are supported with built-in indexes from the source.

Use a reference annotation GTF input from the history instead. All UCSC genome builds with a gene annotation track will have these available in their Downloads area.

@jennaj

The hg38 reference annotation GTF is now best sourced from UCSC. Not from the Table Browser but from the Downloads area here . There are a few Gene tracks to choose from. You can review what each of those represents then upload the selected GTF to Galaxy with the Upload tool. Just copy and paste in the URL and leave all other settings at the default. The correct datatype will be assigned.

The path to the data is similar for all genome builds: https://hgdownload.soe.ucsc.edu/goldenPath/<database>/bigZips/genes/

• For pig genomes, start here UCSC Genome Browser Downloads. The database/dbkey used at UCSC the same as you will see as the assigned “database” to your outputs from upstream steps (BAM) in Galaxy. Be sure not to mix different builds in the same analysis or expect weird results!

FAQ:

Galaxy Training