Hello Kenneth,

Most tools that use a reference genome will accept a custom reference genome, including the visualization tool to create a custom browser. The recommendation is to:


1 - load the genome in FASTA format into your working history using FTP

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

2 - on the target tool form, use the custom reference genome option
    (aka genome "from the history")

Best practice is to use the same custom reference genome dataset for all analysis steps to avoid format/identifier problems. If annotation files (GTF, etc.) are incorporated, be certain to double check that the chromosome/scaffold identifiers are an exact match, and modify if necessary, before use.

Please let us know if you would like more help,

Best,

Jen
Galaxy team



On 1/6/12 10:10 AM, Kenneth McDowall wrote:
Hi,

Would be grateful I the following genomes were uploaded into Galaxy

/Streptomyces coelicolor/A3(2) ;
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Streptomyces_coelicolor_A3_2__uid57801/NC_003888.gbk

/Propionibacterium acnes /KPA171202 (pre-salt downshift);
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Propionibacterium_acnes_KPA171202_uid58101/NC_006085.gbk

Thanks in advance,

Kenneth

*Dr Kenneth McDowall **à**Astbury Centre for Structural Molecular Biology*

Tel +44 (0) 113 343 3109 or Mob. 0783 793 5384 | Ext 33109 |
k.j.mcdow...@leeds.ac.uk <mailto:k.j.mcdow...@leeds.ac.uk> |
www.fbs.leeds.ac.uk

**

*IMCB Director of Taught Programmes **à**Institute of Molecular and
Cellular Biology*

Faculty of Biological Sciences| University of Leeds| Manton Building
Room 10.05 | Leeds LS2 9JT | UK

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