Re: [galaxy-user] Add Reference Genome
Hi Aman, For TopHat, the option is named: "Will you select a reference genome from your history or use a built-in index?:" set this to be "Use one from the history" and the form with refresh. The option named: "Select the reference genome:" will now contain all history datasets of the appropriate format, rather than a list of native indexed dataset names. This is where you would select your reference genome, that is a fasta format dataset, in your history. Take care, Jen Galaxy team On 1/16/12 7:58 PM, Amandeep Sidhu wrote: 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" 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 -- 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/
Re: [galaxy-user] Add Reference Genome
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" 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/
Re: [galaxy-user] Add Reference Genome
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/
