Reference genome absent

Question: Reference genome absent

4.5 years ago by

United States

santydolby • 0 wrote:

Dear Biostar,

For mapping our paired end reads against horse, we are unable to find a reference Equine genome in the drop down menu (Bowtie 2 page) for the genome of interest. Would you be able to guide us regarding this?

The text below this drop down menu says "If your genome of interest is not listed, contact the Galaxy team."

I appreciate any help in this regard.

Thanks a lot!

Sincerely,

Santosh Kumar T K

santoshkumartk@cvm.msstate.edu

Research Associate - I

Equine

Department of Clinical Sciences

College of Veterinary Medicine

Mississippi State University

(662)-312-8836

rna-seq alignment bowtie genomerequest • 1.0k views

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modified 4.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.5 years ago by santydolby • 0

4.5 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

Hi Santosh,

If you could, please see (and comment appropriately on) https://trello.com/c/mJWnAuuQ/1511-to-request-reference-genome-comment-on-this-card

It's also worth noting that you can use a custom genome immediately, without waiting for us to update the server-side stuff. For instructions, please see https://wiki.galaxyproject.org/Learn/CustomGenomes

ADD COMMENT • link written 4.5 years ago by Dannon Baker ♦ 3.7k

4.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

All of Dannon's comments are great - but you may be able to skip the Trello card and just watch the board. The UCSC equCab1 & equCab2 genomes are already on our list for additions in the July/Aug time-frame. When these genomes go out (with the others planned, tentative plans are to include most if not all of the remainder of UCSC mammals and vertebrates), the list of genomes published with new/updated content will be sent to the public Development Trello board. Each will include full indexes for all tools, including Bowtie2/Tophat2, pending any processing issues.

Our working genome list is not published while in planning/staging to leave room for us to manage changes in content. But please feel free to ask (this applies to anyone curious).

This particular genome is right on the edge of being a good candidate for a custom reference genome choice (due to size). Give it a try. If memory problems arise, a cloud Galaxy with the genome installed natively would be the path forward for now. If or when you need help with that, please let us know and we can share some help links from our wiki.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k

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