Question: Could You Please Add Vibrio Cholerae O1 Biovar Eltor Str. N16961 To The Reference Genome?
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gravatar for Tao Dong
6.9 years ago by
Tao Dong10
Tao Dong10 wrote:
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">
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ADD COMMENTlink modified 6.9 years ago by Jennifer Hillman Jackson25k • written 6.9 years ago by Tao Dong10
0
gravatar for Jennifer Hillman Jackson
6.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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
ADD COMMENTlink written 6.9 years ago by Jennifer Hillman Jackson25k
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