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,
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