How to add and use a custom reference genome

Question: How to add and use a custom reference genome

6 months ago by

bass • 0

bass • 0 wrote:

How to import my genome (maize B73v3) into galaxy? I have B73v3 in custom-run UCSC genome browser, how do I load that version into Galaxy so I can use my data track tools to explore? I am new to galaxy, but have successfully done this with hg38/38 (but there was a pull down menu for it) - my ucsc genome browser is genomaize.org - thanks HWB

fasta build genome galaxy custom • 344 views

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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by bass • 0

6 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you are using a public Galaxy server, then the way to use custom genomes is to load them up in fasta format.

FAQ: https://galaxyproject.org/support/

Preparing and using a Custom Reference Genome or Build https://galaxyproject.org/learn/custom-genomes/

Thanks! Jen, Galaxy team

ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

6 months ago by

bass • 0

bass • 0 wrote:

I've loaded a fasta file into my history as a data set - looking for advice & help videos I see "set the tool form's option to use custom genome from history" I can not find anything called tool form options ... (?) how should I proceed? I would like my genome (maize b73v3) which is running on my ucsc browser to show up in the pull-down menu for available genomes - even better, if galaxy would load maizeb73v3 and maizeb73v4 it would be great -it's a multi-billion industry (maize) in US - can I also request that ? thanks again HWB

ADD COMMENT • link written 6 months ago by bass • 0

The term "tool for options" means the parameters set on a tool form.

To use a custom genome, when selecting a reference genome to map against, click on the select menu for that target genome parameter (differs between tools) to use a genome "from the history". The custom genome in fasta format (and assigned to that datatype) will become available. Galaxy will create any indexed need for that tool as part of the overall job.

Please watch this short video for an example: https://vimeo.com/123108417

More built-in genomes/indexed will be added to the server soon -- we are working on an updated process. Maize has already been requested, but we can specify/consider these two builds if you can share back the exact source for both (it must be from an open public data repository). I was only able to find the original build with a quick look at Ensembl but may have missed the others. NCBI is the preferred source if available there. I didn't compare the builds between the sources, but you would know this species and the best data resources better than I.

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

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