Adding A Reference Genome

Question: Adding A Reference Genome

7.4 years ago by

Greetings, My apologies for a what is a naive question, but I would like to map NGS reads to a genome that isn't currently in the list of reference geneomes (soybean, Glycine max). To the guys at Galaxy - can this be added to the list? Or can someone explain to a bioinformatics ignoramus how I would install it in my history? Thanks for your help. Sincerely, Jeremy Coate

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modified 6.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.4 years ago by Jeremy Coate • 70

7.4 years ago by

Kelly Vincent • 340

Kelly Vincent • 340 wrote:

Jeremy, You can definitely ask for new genomes. We frequently add them. This particular genome is already on my working list--we've run into a bit of a snag involving permissions and are trying to figure it out. So I can't promise it will be added or say when if it will be. If you do want to upload it yourself into your history, you need to get the FASTA file. Then when you run a mapper, use this FASTA from your history as the reference file (the run will take longer than it would with a built-in reference would because it has to index the reference). If you need more specific details about getting the FASTA, let us know. Thanks, Kelly

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6.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello David, We can add this genome to the list to be indexed and added, but for immediate use, simply adding as a custom genome would be the quickest and easiest way to gain access and start using the the genome with tools right now. This also gives you some control over the source: match up the genome source with the GTF file source you plan to use. This can avoid having to rename the chromosome identifiers (they must be an exact match between the two). Instructions are here for custom genomes: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome And some RNA-seq links, to help with planning the experiment: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results (see 'Tools on the Main server: Example') Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

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