Ce6/Ws190 Bowtie Index

Question: Ce6/Ws190 Bowtie Index

7.7 years ago by

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

alignment bowtie • 792 views

ADD COMMENT • link •

modified 7.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.7 years ago by giovanni stefani • 30

7.7 years ago by

David Matthews • 630

United Kingdom

David Matthews • 630 wrote:

Hi, Does anyone know how to get a consensus genome from NGS data indicating the percent variance at each nucleotide? I have a small virus genome with manyfold coverage from my transcriptomic run. I'd like to know what the transcriptome indicates is the actual genome plus get a feel for any hotspots where there appears to be significant varience from the reference sequence (i.e. because the reference is wrong or perhaps because of frequent errors in that region due to RNA pol II having a problem accurately transcribing the sequence). Many thanks! David

ADD COMMENT • link written 7.7 years ago by David Matthews • 630

7.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.6 years ago by Jennifer Hillman Jackson ♦ 25k

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.6 years ago by Jennifer Hillman Jackson ♦ 25k

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.6 years ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »