macaca fascicularis genome

Question: macaca fascicularis genome

4.2 years ago by

France

veereshagy • 0 wrote:

Dear Sir/Madam

My name is Veeranagouda Yaligara. We are interested in Identification of novel Bio-markers in Monkey. Galaxy don't have macaca fascicularis genome. I am wondering, is it possible to add macaca fascicularis genome to Galaxy? Genome is available in NCBI.

Also I am wondering, is it possible to add tool to generate contig from FASTQ files?

Thanks in advance.

Kind regards

Veeranagouda Yaligara

Postdoctoral researcher in Sanofi

assembly tool genome • 1.0k views

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modified 4.2 years ago by Martin Čech ♦♦ 4.9k • written 4.2 years ago by veereshagy • 0

4.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This genome is not yet available on the public Main Galaxy instance, because UCSC has not formally released it. When we do add it, it will be as "macFas5". Is this what you are looking for? See the UCSC test browser for the initial browser: http://genome-test.cse.ucsc.edu/

Meanwhile, you can use the genome as a Custom reference genome with nearly all tools (create a Custom Build, if database needs to be assigned).
http://wiki.galaxyproject.org/Support#Custom_reference_genome

If you are working on another Galaxy instance, the administrator of that instance will need to be contacted. Or, you may be able to use the Custom Reference Genome feature there, if enabled (the admin will be also able to answer questions about this, if it doesn't appear to be).

I will look more into this particular genome and find out if an early release copy can be obtained from UCSC. Sticking with the same version of the genome through all analysis steps is always best, especially when reference annotation data is needed (now or later). This avoids conflicts with chromosome name identifiers. If we are able to include it, I'll post back here with a link to a ticket you can follow to track progress.

But don't wait for us, this can take time. Go forward with the custom reference option for now.

Tools for assembly can be found in the Tool Shed, for use in a local or cloud Galaxy. Please see:

http://usegalaxy.org/toolshed
https://wiki.galaxyproject.org/BigPicture/Choices

Best, Jen, Galaxy team

ADD COMMENT • link modified 4.2 years ago • written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k

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