Dear Jennifer, Top hat does does not have the option of using custom genomes from history like other tools. It says that if reference genome needs to be added contact galaxy team.
Thanks. Regards, Aman. ------------ Sent from Aman's iPad @biomap | http://amandeep.org/ | http://biomap.org/ On 17/01/2012, at 10:37, "Jennifer Jackson" <j...@bx.psu.edu> wrote: > Hello Aman, > > The quickest way to use new genomes with tools is to use them as a custom > reference genome. To do this, load the genome in fasta format into your > history and set the tool form option to use the reference genome "from the > history". > > Best practices: > 1 - double check that the format is strict fasta (all lines wrapped to same > length, no extra lines or hidden characters, sequence identifiers are unique). > 2 - use the same genome dataset for all steps within an analysis > 3 - load using FTP and make certain load is complete > http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP > > Hopefully this helps! > > Best, > > Jen > Galaxy team > > On 1/14/12 6:32 PM, Amandeep Sidhu wrote: >> Hi All, >> >> We need Vicugna Pacos (http://asia.ensembl.org/Vicugna_pacos/Info/Index) >> added as a reference genome to run analysis using Top Hat on the public >> server. >> >> Thanks. >> >> Regards, >> Aman. >> >> ------------ >> Sent from Aman's iPad >> @biomap | http://amandeep.org/ | http://biomap.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/ > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/Support > ___________________________________________________________ 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/
