liftOver from scaffold to genome assembly

[Saroja Somasundaram]

Hi,

Thanks for the support with UCSC browser. I would like to lift over bedGraph files from marmoset scaffold assembly (https://www.ncbi.nlm.nih.gov/assembly/GCA_002754865.1/) to latest marmoset assembly in UCSC - CalJac3. How should I go about making a chain file for this?

Thanks,

Saroja

[Matthew Speir]

Hello, Saroja.

Thank you for your question about creating a LiftOver file to convert coordinates between two assemblies.

To create a LiftOver chain file to convert coordinates between two assemblies of the same organism, you can use the script and instructions that we describe on this genomewiki page: http://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html
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Matthew Speir

User Experience, Quality Assurance and User Support

HCA, CIRM, and UCSC Genome Browser

UCSC Genomics Institute

[Saroja Somasundaram]

Thanks Matthew. Is there also a script to do the same from marmoset scaffold assembly (https://www.ncbi.nlm.nih.gov/assembly/GCA_002754865.1/) to human hg38 in UCSC?

Best,

Saroja  

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From: Matthew Speir <msp...@soe.ucsc.edu>
Sent: Monday, March 23, 2020 11:00 AM
To: Saroja Somasundaram <sar...@alleninstitute.org>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] liftOver from scaffold to genome assembly

 

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[Luis Nassar]

Hello Saroja,

We do have a separate script/process for assemblies that are not the same species (http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl):

• DoBlastzChainNet.pl - which is focused on creating chains between two assemblies from different organisms (e.g. mouse mm10 and human hg38)
  • This answer to one our previous mailing list questions may be provide a good starting point: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/Tvk9wj59P2M/oAxgKLknDQAJ

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/MW2PR12MB2443D08088F25DEA49107F89CAF00%40MW2PR12MB2443.namprd12.prod.outlook.com.