Browser Chrom/Plasmid NameLength (bp)GC Content (%)Gene CountNCBI RefSeq AccessionchrI<http: microbes.ucsc.edu="" cgi-="" bin="" hgtracks?db="vibrChol1&amp;position=chrI:1-2961149"> 296114947.692888NC_002505<http: www.ncbi.nlm.nih.gov="" entrez="" viewer.fc="" gi?val="NC_002505"> chrII<http: microbes.ucsc.edu="" cgi-="" bin="" hgtracks?db="vibrChol1&amp;position=chrII:1-1072315"> 107231546.911119NC_002506<http: www.ncbi.nlm.nih.gov="" entrez="" viewer.fc="" gi?val="NC_002506">

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support