Chain file creation

[Ciro Ramirez Suastegui]

Dear UCSC Genome Browser Team,

We are interested in the creation of a Chain file from two genome references (an unmodified assembly and a custom one). We were wondering if you could provide a way of achieving this given that it's too specific and it's not possible to find this instance in your chain folder.

Best Regards,

Ciro

[Matthew Speir]

Hello, Ciro.

Thank you for your question about creating chain alignments between two assemblies.

We provide two scripts that may be of use here:

• DoBlastzChainNet.pl - which is focused on creating chains between two assemblies from different organisms (e.g. mouse mm10 and human hg38)
• If this is what you're after, then this answer to one our previous mailing list questions may be of interest: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/Tvk9wj59P2M/oAxgKLknDQAJ
• DoSameSpeciesLiftOver.pl - which is focused on creating chains between two assemblies of the same organism (e.g. human hg19 and human hg38)
• The following page of our wiki details how to use this script: 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

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Matthew Speir

User Experience, Quality Assurance and User Support

HCA, CIRM, and UCSC Genome Browser

UCSC Genomics Institute