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Question: Rna-Seq With Staphylococcus Aureus Strain Newman
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gravatar for Joe Harrison
7.1 years ago by
Joe Harrison • 20
Joe Harrison • 20 wrote:
Hello, Would you please add Staphylococcus aureus strain Newman to your database? Workflows to analyze data for genomes available through your database are really simple - but I must admit that I've been struggling with trying to get this to work for a genome (and in particular with the annotation) that I've uploaded myself. Thanks for the help and the continued support! Joe Joe J. Harrison Senior Fellow Department of Microbiology University of Washington
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modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by Joe Harrison • 20
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gravatar for Jennifer Hillman Jackson
7.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Joe, The genome is already included in Galaxy. Click on the pencil icon for a dataset and search with the term "Staphylococcus" and search through the entries to locate: Staphylococcus aureus subsp. aureus str. Newman (18801) The short label database will be set to "18801". This is how the UCSC Microbial database content was set up originally and we decided it was best not to change it. If you would like help solving issues with annotation files and the reference genome (native or uploaded, please let us know. Quick list of things to check: 1 - database short name is same every place it is used (as the assigned "database" + content within a dataset). 2 - chromosome/contig identifiers are the the same every place they are used. Even minor differences such as capitalization must be normalized. 3 - data coordinates are with respect to the forward strand and have a zero-based start (for most formats, as noted in the format specification). Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k
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