This directory contains reciprocal-best netted chains for calJac1-rheMac2.

 - calJac1.rheMac2.rbest.net.gz: calJac1-referenced recip.best net to rheMac2.
 - calJac1.rheMac2.rbest.chain.gz: chains extracted from the recip.best
   net.  These can be passed to the liftOver program to translate coords
   from calJac1 to rheMac2 through the recip.best net.

 - rheMac2.calJac1.rbest.net.gz: rheMac2-referenced recip.best net.
 - rheMac2.calJac1.rbest.chain.gz: recip.best "liftOver" chains.
 - axtRBestNet/calJac1.rheMac2.rbest.axt.gz: chained and netted alignments,
   i.e. the best chains in the Marmoset genome, with gaps in the best
   chains filled in by next-best chains where possible.  Only alignments
   that are reciprocal best are kept.  The axt format is
   described in http://genome.ucsc.edu/goldenPath/help/axt.html .