Request To Add Reference Genome

Question: Request To Add Reference Genome

7.0 years ago by

Hello Galaxy Team, I am writing to request that the genome of *Sinorhizobium meliloti *1021 be added to the "Map with Bowtie for Illumina" tool. I am using the main server http://main.g2.bx.psu.edu/ and my user name is mbiggs. Please let me know if this email is received. Thanks, Matt Biggs

alignment bowtie • 655 views

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modified 7.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.0 years ago by Matthew Biggs • 10

7.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Matt, The quickest way to use new genomes with most tools, including Bowtie, is to use them as a custom reference genome. To do this, load the genome in fasta format into your history. Then, on the tool form (for Bowtie, will vary slightly between tools), set: Will you select a reference genome from your history or use a built-in index?: "Use one from the history" The form will refresh, them set: Select the reference genome: "dataset_for_your_loaded_genome" Best practice: 1 - double check that the format is strict fasta (all lines wrapped to same length, no extra lines or hidden characters, sequence entries are unique within file). 2 - use the same genome dataset for all steps within an analysis 3 - load using FTP and make certain load is complete http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP Hopefully this helps! Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.0 years ago by Jennifer Hillman Jackson ♦ 25k

7.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Matt, I am not sure what you mean by an annotated genome, would you be able to send more details? Meanwhile, I can let you know that the tools that use a reference genome (custom or native) all expect a fasta formatted input and use the data directly or create indexes from the data. Any DNA (and sometime RNA) nucleotide fasta file can be used and whether using something other than a complete genome makes sense scientifically is up to the user to determine. Thanks! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.0 years ago by Jennifer Hillman Jackson ♦ 25k

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