Question: Adding A Reference Genome
gravatar for Jeremy Coate
7.4 years ago by
Jeremy Coate70
Jeremy Coate70 wrote:
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
galaxy • 719 views
ADD COMMENTlink modified 6.2 years ago by Jennifer Hillman Jackson25k • written 7.4 years ago by Jeremy Coate70
gravatar for Kelly Vincent
7.4 years ago by
Kelly Vincent340
Kelly Vincent340 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
ADD COMMENTlink written 7.4 years ago by Kelly Vincent340
gravatar for Jennifer Hillman Jackson
6.2 years ago by
United States
Jennifer Hillman Jackson25k 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: And some RNA-seq links, to help with planning the experiment: (see 'Tools on the Main server: Example') Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.2 years ago by Jennifer Hillman Jackson25k
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