I'm trying to translate this command line run into the Galaxy GUI but
I'm not seeing a place to specify the .gtf file.
Does anyone know?
tophat2 -p 8 -G /groups/bowtie2_index/mRNA.gtf -o /groups/hp_1
Open up "TopHat settings to use:" to "Full Parameter list" to find the
option: "Use Own Junctions:" and set this to "Yes". There will be a
option underneath it for "Use Gene Annotation Model:" - which is where
the GTF file is entered when set to "Yes".
Hopefully this helps,