Create Chain File

Question

[danielcook2013]

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

Thanks!

Answer 1

[Pierre Lindenbaum]

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.