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>

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