Question: Is the gene model file and gene annotation file in the Galaxy the same?
0
gravatar for lilin1206
2.1 years ago by
lilin12060
lilin12060 wrote:

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!

rna-seq • 881 views
ADD COMMENTlink modified 2.1 years ago by lieven.sterck10.0k • written 2.1 years ago by lilin12060
2
gravatar for lieven.sterck
2.1 years ago by
lieven.sterck10.0k
VIB, Ghent, Belgium
lieven.sterck10.0k wrote:

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

ADD COMMENTlink written 2.1 years ago by lieven.sterck10.0k

Got it! Thanks a lot!

ADD REPLYlink written 2.1 years ago by lilin12060
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1413 users visited in the last hour
_