Hi Xiaojing, You'll need to make sure that the dbkey of your input BAM file is set to a genome build that has data available. Click the pencil icon to set the genome build. If you have set the genome build, but still have an empty select box then data may not be available for this build/tool combination, you can request that the needed data be added for this tool. If your reference genome is not available, you can also upload a FASTA file containing the genome and access it directly from the history.
Thanks for using Galaxy, Dan On Aug 17, 2011, at 11:26 AM, Hong, Xiaojing wrote: > Hi, > > I just uploaded the BAM file for an exome sequencing sample and was trying to > use the GATK tools. In the first step, realigner Target creator, I can see my > uploaded file but I can’t see any options under the “using reference genome” > and the following choices so I can’t click execute. Did I do anything wrong? > Thanks! > > Xiaojing Hong > University of Iowa > > > ___________________________________________________________ > 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/
___________________________________________________________ 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/
