Question: Could You Please Add Vibrio Cholerae O1 Biovar Eltor Str. N16961 To The Reference Genome?
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:"" cgi-="" bin="" hgtracks?db="vibrChol1&amp;position=chrI:1-2961149"> 296114947.692888NC_002505<http:"" entrez="" viewer.fc="" gi?val="NC_002505"> chrII<http:"" cgi-="" bin="" hgtracks?db="vibrChol1&amp;position=chrII:1-1072315"> 107231546.911119NC_002506<http:"" entrez="" viewer.fc="" gi?val="NC_002506">
ADD COMMENTlink modified 6.9 years ago by Jennifer Hillman Jackson25k • written 6.9 years ago by Tao Dong10
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: 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 Best wishes for your project, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.9 years ago by Jennifer Hillman Jackson25k
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