Medicago And Soybean Genome In Galaxy

5.7 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Oswaldo, The soybean genome is already on our list of genomes to consider for addition and was included on an internal list, that I have not put out on our public development board: https://trello.com/card/reference-genome- requests/506338ce32ae458f6d15e4b3/239 You can track progress through this ticket by following it. I can let you know that in the immediate term (next month), these are probably not going to be done. But I can't say much beyond that - things change fast. To have Medicago truncatula added, we need it to be in a somewhat finshed state and preferably to have an NCBI project. If you can send me the project ID, plus actual accession including the accession of any mito/chloro to included, we can add to the ticket above. No promises, but at least that puts it on the list, with build specificity. Meanwhile - the best news is that you don't have to wait for us at all - you can start using this data right away with tools. Simply load the genomes in fasta format into your history as datasets and use them as custom genomes with tools that way. In fact, you may find this is a better solution. You can even use a custom genome with visualizations within Galaxy. Full instructions are here: http://wiki.galaxyproject.org/Support#Custom_reference_genome Take care, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.7 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I have the same question. I want to use the Bowtie2 - map reads against reference genome (Galaxy Version 2.3.4.2) in Galaxy and in the list to select the reference genome Medicago truncatula is not in the list. It is gonna be available in the future? Thank you!

ADD REPLY • link modified 2 days ago • written 2 days ago by soledad.perezsantangelo • 0

Hi,

For now, use the genome as a Custom genome. The link above redirects to the updated Galaxy Hub FAQ page. The other FAQ is important to review if you are including reference annotation in your analysis. https://galaxyproject.org/support/

Preparing and using a Custom Reference Genome or Build https://galaxyproject.org/learn/custom-genomes/
Mismatched Chromosome identifiers (and how to avoid them) https://galaxyproject.org/support/chrom-identifiers/

We are working to incorporate more plant genomes, some in collaboration with other community groups. This is a large project that needed some development work to support it first and that is mostly done now. I added your genome to the tracking ticket we keep for requests here: https://github.com/galaxyproject/galaxy/issues/1470#issuecomment-441831629

Should ELIXER not include it indexed already (where we plan to source most plant genomes as they have been already been curated and paired with reference annotation very nicely), we might request that they add it, or go ahead and index it independently. I included that info the ticket as a to-do item.

If you have the NCBI accession/version information, please post that back, so we can be sure match up the right data, and I'll add it to the Github ticket. Or you can add it back there as another comment if you want. Please be as specific as possible about the desired content (mito and chroro are sometimes in a different record from the base chromosomes).

Thanks! Jen

ADD REPLY • link written 2 days ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen. Thank you so much for the quick reply. I will look for the information and post it back here, as specific as possible. Thank you again. Cheers Sol

ADD REPLY • link written 2 days ago by soledad.perezsantangelo • 0

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