Question: Ce6/Ws190 Bowtie Index
gravatar for giovanni stefani
7.7 years ago by
giovanni stefani30 wrote:
Hello everybody, I would like to download the C. elegans ce6/WS190 bowtie index (six .ebwt files and the 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 COMMENTlink modified 7.6 years ago by Jennifer Hillman Jackson25k • written 7.7 years ago by giovanni stefani30
gravatar for David Matthews
7.7 years ago by
United Kingdom
David Matthews630 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 COMMENTlink written 7.7 years ago by David Matthews630
gravatar for Jennifer Hillman Jackson
7.6 years ago by
United States
Jennifer Hillman Jackson25k 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!). To create the files for use with TopHat in Galaxy, please see these instructions in our wiki: scroll to: "Setting Up the Reference Genomes for NGS Tools" Best! Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 7.6 years ago by Jennifer Hillman Jackson25k
ADD REPLYlink written 7.6 years ago by Jennifer Hillman Jackson25k
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
ADD REPLYlink written 7.6 years ago by Jennifer Hillman Jackson25k
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