Question: Convert genome coordinates between assemblies and genomes (Galaxy Version 1.0.5) aka LiftOver
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gravatar for devikaparvathy
8 weeks ago by
devikaparvathy10 wrote:

I have two related bacterial genomes of same species - different subspecies. I want to map the co-ordinates of one genome to the other. How do I use the Liftover tool in galaxy for this? What format of the target organism genome is required?

Note: I have the gff file and FASTA files of both the source and target organism genomes. I uploaded them to galaxy and selected the source organism gff for the column "Convert coordinates of".

But the second column "To" says "No options available". What type of file for the target genome am I supposed to provide?

ADD COMMENTlink modified 7 weeks ago by Jennifer Hillman Jackson23k • written 8 weeks ago by devikaparvathy10
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gravatar for Jennifer Hillman Jackson
7 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Mapping coordinates between assemblies utilize base data sourced from UCSC. Specifically, the liftOver components of the primary "Conservation" track. If UCSC has not mapped the two genomes, then this data will be unavailable (at the UCSC web or line-command version of the tool or in the Galaxy wrapped version). Bacterial genomes are not included in this data.

The process UCSC runs to generate this data is quite complex, yet if you are willing to try, then those data could be used with the tool in your own local, docker, or cloud Galaxy. Please contact UCSC for the most current data generation procedures and other recommendations they may have: http://genome.ucsc.edu. See the Help pages for contact information. Their google group is most likely where you will want to search for prior Q&A on the topic and can ask a new question if not covered already with the detail you need.

Once you have an appropriate lifeOver reference file, this can be loaded into your local Galaxy. The genomes must also be installed as native indexed genomes. Use a fetch genome Data Manager to add the genome itself, then add in the liftover index (manually). The .loc file for existing liftover indexes (from the Galaxy rsync server) can be used as an example to model after link in your custom index. There is no Liftover Data Manager yet, but one is in development.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 7 weeks ago by Jennifer Hillman Jackson23k
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