Re: [galaxy-user] How to Provide .gtf file to tophat2
That's very helpful! Thanks. -Greg On Tue, Dec 18, 2012 at 11:39 AM, Jennifer Jackson wrote: > Hello Greg, > > 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 new > option underneath it for "Use Gene Annotation Model:" - which is where the > GTF file is entered when set to "Yes". > > Hopefully this helps, > > Jen > Galaxy team > > > On 12/18/12 8:10 AM, greg wrote: >> >> 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 >> /groups/genome /groups/reads.fastq >> >> thanks, >> >> Greg >> ___ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >>http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >>http://lists.bx.psu.edu/ > > > -- > Jennifer Jackson > http://galaxyproject.org > ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] How to Provide .gtf file to tophat2
Hello Greg, 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 new option underneath it for "Use Gene Annotation Model:" - which is where the GTF file is entered when set to "Yes". Hopefully this helps, Jen Galaxy team On 12/18/12 8:10 AM, greg wrote: 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 /groups/genome /groups/reads.fastq thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] How to Provide .gtf file to tophat2
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 /groups/genome /groups/reads.fastq thanks, Greg ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
