Hello Tao,

This genome is labeled in Galaxy as:

Vibrio cholerae O1 biovar eltor str. N16961 (vibrChol1)

However, I am guessing that the genome is not indexed for the tools you want to use it with. This means that you will need to use it as a custom reference genome. The first step is to obtain a fasta version of the genome (from either Genbank or UCSC), then upload it into your working history using FTP, and finally to use the dataset as a custom reference genome with tools (option is usually called "using a reference from the history" on tool form).

FTP help: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

To contact UCSC about microbial genome source data downloads (Galaxy does not maintain a genome source data service), please see the contact information for the Lowe lab on the UCSC Microbial browser home page (credits section) at http://microbes.ucsc.edu/.

Best wishes for your project,

Jen
Galaxy team

On 1/19/12 7:17 AM, Tao Dong wrote:
Browser Chrom/Plasmid Name      Length (bp)     GC Content (%)  Gene Count      
NCBI
RefSeq Accession
chrI
<http://microbes.ucsc.edu/cgi-bin/hgTracks?db=vibrChol1&position=chrI:1-2961149>
        2961149 47.69   2888    NC_002505
<http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_002505>
chrII
<http://microbes.ucsc.edu/cgi-bin/hgTracks?db=vibrChol1&position=chrII:1-1072315>
        1072315 46.91   1119    NC_002506
<http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_002506>



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to