On Wed, Apr 20, 2011 at 4:00 AM, Edward Dudley egd...@psu.edu wrote:
Hi -
I have a set of 454 reads that have been trimmed and converted to BAM format
using Galaxy, and I can visualize the alignment with E. coli genomes using
the UCSC browser. Problem is, I'd like to display the alignment in
Are you downloading the ³BAI² index file, as well?
That might be the problem.
Best,
Ann
On 4/19/11 11:00 PM, Edward Dudley egd...@psu.edu wrote:
Hi -
I have a set of 454 reads that have been trimmed and converted to BAM format
using Galaxy, and I can visualize the alignment with E. coli
Hello all. I am re-exploring Galaxy after a year hiatus. While I searched
the archives to no avail it is possible that my question/complaint was already
answered. If so, please ignore.
I find the placement of Mouse-ear Cress (arabidopsis) in the 'select a
reference genome' list to be
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,
Dear Ann and Jeremy:
We have this discussion long time ago, and I am sorry that I brought it
up here
again. I am just thinking that as Ann said, can we add this tool which convert
bam into wig file into galaxy? Or make a workflow to generate a wig
file from a
bam file generate by tophat? In
Vasu,
Here are the steps to create this visualization; this is relatively new
functionality, and you'll want to use our test server (
http://test.g2.bx.psu.edu/ ) for now.
(1) Create a new visualization from the main menu: Visualization -- New Track
Browser and choose your genome build.
(2)
Hi Ying,
You're in luck because I've been working with genome browsers lately, so I
think I can help you address your problem. What you're looking for is a
visualization of a coverage histogram for the BAM reads produced by Tophat,
yes?
It turns out that some genome browsers provide this
I can answer IGV questions, sadly I'm still coming up to speed on
Galaxy.
I've lost track of the original question, but IGV computes a coverage
histogram on the fly, a bit like the Galaxy Track Browser, but you
have to be zoomed in. However, you can also precompute a coverage
Hi everyone,
I'd like to know if i can receive digested mail only. Thanks
Sincerely,
John
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