This directory contains reciprocal-best netted chains for droSim1-droYak2.

 - droSim1.droYak2.rbest.net.gz: droSim1-referenced recip.best net to droYak2.
 - droSim1.droYak2.rbest.chain.gz: chains extracted from the recip.best 
   net -- these can be passed to the liftOver program to translate coords 
   from droSim1 to droYak2 through the recip.best net.

 - droYak2.droSim1.rbest.net.gz: droYak2-referenced recip.best net.
 - droYak2.dm2.rbest.chain.gz: recip.best "liftOver" chains.

Here is how these files were generated, starting with the file 
droSim1.droYak2.over.chain.gz which can be downloaded as
http://hgwdev.cse.ucsc.edu/goldenPath/droSim1/liftOver/droSim1ToDroYak2.over.chain.gz
and files which we call "chrom.sizes" locally but which can be downloaded as 
chromInfo.txt.gz in the database/ subdir on our main download server,
hgdownload.cse.ucsc.edu.  

    # Swap droSim1-best chains to be droYak2-referenced:
    chainStitchId droSim1.droYak2.over.chain.gz stdout \
    | chainSwap stdin stdout \
    | chainSort stdin droYak2.droSim1.tBest.chain
    # Net those on droYak2 to get droYak2-ref'd reciprocal best net:
    chainPreNet droYak2.droSim1.tBest.chain \
      /cluster/data/{droYak2,droSim1}/chrom.sizes stdout \
    | chainNet -minSpace=1 stdin /cluster/data/{droYak2,droSim1}/chrom.sizes \
        stdout /dev/null \
    | netSyntenic stdin droYak2.droSim1.rbest.net
    # Extract droYak2-ref'd reciprocal best chain:
    netChainSubset droYak2.droSim1.rbest.net droYak2.droSim1.tBest.chain stdout \
    | chainStitchId stdin droYak2.droSim1.rbest.chain
    # Swap to get droSim1-ref'd reciprocal best chain:
    chainSwap droYak2.droSim1.rbest.chain stdout \
    | chainSort stdin droSim1.droYak2.rbest.chain
    # Net those on droSim1 to get droSim1-ref'd reciprocal best net:
    chainPreNet droSim1.droYak2.rbest.chain \
      /cluster/data/{droSim1,droYak2}/chrom.sizes stdout \
    | chainNet -minSpace=1 -minScore=0 \
      stdin /cluster/data/{droSim1,droYak2}/chrom.sizes stdout /dev/null \
    | netSyntenic stdin droSim1.droYak2.rbest.net
    # Compress and clean up.
    rm droYak2.droSim1.tBest.chain
    gzip *.rbest.*
    md5sum *.rbest.*.gz > md5sum.txt