This directory contains reciprocal-best netted chains for calJac4-hg38.

 - calJac4.hg38.rbest.net.gz: calJac4-referenced recip.best net to hg38.
 - calJac4.hg38.rbest.chain.gz: chains extracted from the recip.best
   net.  These can be passed to the liftOver program to translate coords
   from calJac4 to hg38 through the recip.best net.

 - hg38.calJac4.rbest.net.gz: hg38-referenced recip.best net.
 - hg38.calJac4.rbest.chain.gz: recip.best "liftOver" chains.

 - axtRBestNet/calJac4.hg38.rbest.axt.gz reciprocal best alignments in
   AXT format

See also, description of AXT format::
    http://genome.ucsc.edu/goldenPath/help/axt.html
description of CHAIN format:
    http://genome.ucsc.edu/goldenPath/help/chain.html
description of NET format:
    http://genome.ucsc.edu/goldenPath/help/net.html