Question: Is the gene model file and gene annotation file in the Galaxy the same?
gravatar for lilin1206
2.1 years ago by
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
gravatar for lieven.sterck
2.1 years ago by
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
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