Question: Create Chain File
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gravatar for danielcook2013
5.6 years ago by
danielcook201370 wrote:

Does anyone know how to construct a chain file from two assemblies for use with UCSCs liftover tool?

Thanks!

liftover • 4.5k views
ADD COMMENTlink modified 5.6 years ago by Pierre Lindenbaum124k • written 5.6 years ago by danielcook201370
1
gravatar for Pierre Lindenbaum
5.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

The process is described here: http://genomewiki.ucsc.edu/index.php/LiftOver_Howto

Creating a liftOver file is very similar to a whole-genome alignment. A liftOver file is a chain file, where for each region in the genome the alignments of the best/longest syntenic regions are used to translate features from one version of a genome to another.

ADD COMMENTlink written 5.6 years ago by Pierre Lindenbaum124k
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