Is the gene model file and gene annotation file in the Galaxy the same?

Question

[lilin1206]

In the galaxy, when I use RNA STAR to map the reads, it requests the "Gene model (gff3,gtf) file for splice junctions", and then when I use the Htseq or featureCounts, it requests the "Gene annotation file or GFF file".

I am wondering whether for this I can use the same GTF file? or one is specific for splice junctions, another is specific for gene names?

Thank you so much!

Answer 1

[lieven.sterck]

Yes, in theory you can swap those files. You just need to make sure they are both correctly formatted and that they contain the same 'naming' : that eg. gene_id is consistently used to denote the genes (and thus not gene_id in file A and parent_id in file B), or adapt your htseq count cmd accordingly.

Those two file types are nothing specifically for splice sites and/or names. They are simply alternatives from each other, they both contain gene annotations in their respected format

[lilin1206]

Got it! Thanks a lot!