This directory contains reciprocal-best netted chains for hg38-calJac3.

 - hg38.calJac3.rbest.net.gz: hg38-referenced recip.best net to calJac3.
 - hg38.calJac3.rbest.chain.gz: chains extracted from the recip.best
   net.  These can be passed to the liftOver program to translate coords
   from hg38 to calJac3 through the recip.best net.

 - calJac3.hg38.rbest.net.gz: calJac3-referenced recip.best net.
 - calJac3.hg38.rbest.chain.gz: recip.best "liftOver" chains.

 - directory axtRBestNet/ - reciprocal best alignments in axt file format
   http://genome.ucsc.edu/goldenPath/help/axt.html