Produce Interspecies Liftover Chain
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9.8 years ago

I'm trying to produce a chain.over file that we can use with UCSC's liftOver program to convert hg19 coordinates to canFam3.0 coordinates. (Yes, I know there's an hg19 to canFam3.1 chain. Our files are in canFam3.0 though... >_<*)

I'm more-or-less following the directions on the UCSC GenomeWiki found here. They work fine if I'm producing an intraspecies chain (canFam2 to canFam3.0, for example), but the results are, of course, unacceptable when I try to produce an interspecies chain as above. The directions say I should use blastz/lastz to do the alignment, so I'd like to try that.

With all of that in mind, how should I run lastz and, where does its output fit into the pipeline described on the GenomeWiki?

liftover hg • 2.5k views

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