Hello Jo,

Please see below

On 6/22/11 1:15 PM, Joanne Rampersad wrote:
Hi
I have a few questions

1. I am trying to use Bowtie to map my data using a reference genome.
the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is
there a way that I can download the file in fasta format to use as a
reference in Tablet?

I can import the SAM output into Tablet if I do not give it a
reference, but I would like to see it with the reference

Galaxy does not currently have genomes available for download. Good sources would be UCSC, NCBI, Ensembl, and other species-specific projects.

2. I have used the Sam to Bam converter and downloaded the file to my
computer then tried to import it into Tablet, but it gives an error.
Does anyone have any advice on doing this?

The best folks to answer Tablet questions would be those tool authors, but that said, a some guesses are that the .bam.bai index file was not loaded along with the .bam? Or maybe the SAM needed to be sorted in some special way first?

3. Does Galaxy have any tools for doing a blast search against a
reference genome or database?

BLAST is not in on the Galaxy main server, but if you want to see how it is incorporated, it is on our test server (but beware if running any serious jobs, this is an active development area and large runs are not permitted). http://test.g2.bx.psu.edu. After testing out the implementation, and you decide that you want to run BLAST on full datasets using Galaxy, then creating a cloud or local instance is the recommendation.
http://getgalaxy.org
http://getgalaxy.or/cloud


Hopefully this is helpful! Thanks for using Galaxy!

Best,

Jen
Galaxy team


Any help/instructions that you point me to is greatly appreciated.


Jo
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___________________________________________________________
The Galaxy User list should be used for the discussion of
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