Re: [galaxy-user] ce6/WS190 bowtie index
Hello again, Apologies for the multiple emails, but to be clear: in Galaxy, Tophat uses the same indexes as Bowtie (i.e. use the Bowtie instructions to get set up). Please let us know if we can help again, Jen On 4/20/11 2:14 PM, Jennifer Jackson wrote: Hello - Few more links that may be helpful: http://bitbucket.org/galaxy/galaxy-central/wiki/DataTables https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies Thanks! Jen On 4/20/11 1:49 PM, Jennifer Jackson wrote: Hello Giovanni, Galaxy does not (yet) support genome downloads, but a recommended source (it was ours) would be the UCSC Genome browser. Here is a link to their downloads ftp site. Instructions are in the README files within the file directories. Be sure to use FTP (direct unix or a client such as FileZilla, a web browser download will fail on a file of this size, as you might already know!). http://hgdownload.cse.ucsc.edu/downloads.html#c_elegans To create the files for use with TopHat in Galaxy, please see these instructions in our wiki: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup scroll to: "Setting Up the Reference Genomes for NGS Tools" Best! Jen Galaxy team On 4/4/11 8:15 AM, giovanni stefani wrote: Hello everybody, I would like to download the C. elegans ce6/WS190 bowtie index (six .ebwt files and the make_c_elegans_ws120.sh) that is in use in galaxy Tophat as reference genome. Is that possible, and how do I go about that? Thank you very much, Giovanni ___ 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 ___ 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] ce6/WS190 bowtie index
Hello - Few more links that may be helpful: http://bitbucket.org/galaxy/galaxy-central/wiki/DataTables https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies Thanks! Jen On 4/20/11 1:49 PM, Jennifer Jackson wrote: Hello Giovanni, Galaxy does not (yet) support genome downloads, but a recommended source (it was ours) would be the UCSC Genome browser. Here is a link to their downloads ftp site. Instructions are in the README files within the file directories. Be sure to use FTP (direct unix or a client such as FileZilla, a web browser download will fail on a file of this size, as you might already know!). http://hgdownload.cse.ucsc.edu/downloads.html#c_elegans To create the files for use with TopHat in Galaxy, please see these instructions in our wiki: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup scroll to: "Setting Up the Reference Genomes for NGS Tools" Best! Jen Galaxy team On 4/4/11 8:15 AM, giovanni stefani wrote: Hello everybody, I would like to download the C. elegans ce6/WS190 bowtie index (six .ebwt files and the make_c_elegans_ws120.sh) that is in use in galaxy Tophat as reference genome. Is that possible, and how do I go about that? Thank you very much, Giovanni ___ 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 ___ 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] ce6/WS190 bowtie index
Hello Giovanni, Galaxy does not (yet) support genome downloads, but a recommended source (it was ours) would be the UCSC Genome browser. Here is a link to their downloads ftp site. Instructions are in the README files within the file directories. Be sure to use FTP (direct unix or a client such as FileZilla, a web browser download will fail on a file of this size, as you might already know!). http://hgdownload.cse.ucsc.edu/downloads.html#c_elegans To create the files for use with TopHat in Galaxy, please see these instructions in our wiki: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup scroll to: "Setting Up the Reference Genomes for NGS Tools" Best! Jen Galaxy team On 4/4/11 8:15 AM, giovanni stefani wrote: Hello everybody, I would like to download the C. elegans ce6/WS190 bowtie index (six .ebwt files and the make_c_elegans_ws120.sh) that is in use in galaxy Tophat as reference genome. Is that possible, and how do I go about that? Thank you very much, Giovanni ___ 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 ___ 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] ce6/WS190 bowtie index
Hello everybody, I would like to download the C. elegans ce6/WS190 bowtie index (six .ebwt files and the make_c_elegans_ws120.sh) that is in use in galaxy Tophat as reference genome. Is that possible, and how do I go about that? Thank you very much, Giovanni ___ 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/
