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[Genome] how to create over.chain files?: [Genome] how to create over.chain files?

Jennifer Jackson jen at soe.ucsc.edu
Wed Jan 13 17:16:03 PST 2010
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Hello,

Here are a few links to some help documents to create this type of file. More is in the README files in the kent source tree. The basic idea to create a chain file between two genomes (the process makes an over.chain file at the same time). Reading the track description in the Assembly browser for Chains is also recommended, as it has Methods, Credits, and links to external tools or related publications.

http://genomewiki.ucsc.edu/index.php/Chains_Nets
http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver

http://genomewiki.cse.ucsc.edu/index.php/The_source_tree
http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities

http://genome.ucsc.edu/FAQ/FAQdownloads#download27
http://genomewiki.cse.ucsc.edu/index.php/Category:Technical_FAQ

Please review and let us know if you have any questions,
Thanks,
Jennifer

------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group

----- "jdidion" wrote:

> From: "jdidion"
> To: genome at soe.ucsc.edu
> Sent: Wednesday, January 13, 2010 2:55:34 PM GMT -08:00 US/Canada Pacific
> Subject: [Genome] how to create over.chain files?
>
> I have used the snp and indel data released by the sanger mouse
> genomes
> project to impute the genomes of the 17 strains being sequenced. Now I
> want
> to map genomic positions between the reference genome and any of the
> 17
> imputed genomes. How do I create an over.chain file so that I can do
> this
> with the liftover tool?
>
> Thanks!
>
> John Didion
> _______________________________________________
> Genome maillist - Genome at lists.soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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