This directory contains reciprocal-best netted chains for dm2-droYak2.

 - dm2.droYak2.rbest.net.gz: dm2-referenced recip.best net to droYak2.
 - dm2ToDroYak2.rbest.chain.gz: chains extracted from the recip.best 
   net -- these can be passed to the liftOver program to translate coords 
   from dm2 to droYak2 through the recip.best net.

 - droYak2.dm2.rbest.net.gz: droYak2-referenced recip.best net.
 - droYak2ToDm2.rbest.chain.gz: recip.best "liftOver" chains.

Here is how these files were generated, starting with the file 
dm2.droYak2.over.chain.gz which can be downloaded as
http://hgwdev.cse.ucsc.edu/goldenPath/dm2/liftOver/dm2ToDroYak2.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 dm2-best chains to be droYak2-referenced:
    chainStitchId dm2.droYak2.over.chain.gz stdout \
    | chainSwap stdin stdout \
    | chainSort stdin droYak2.dm2.tBest.chain
    # Net those on droYak2 to get droYak2-ref'd reciprocal best net:
    chainPreNet droYak2.dm2.tBest.chain \
      /cluster/data/{droYak2,dm2}/chrom.sizes stdout \
    | chainNet -minSpace=1 stdin /cluster/data/{droYak2,dm2}/chrom.sizes \
        stdout /dev/null \
    | netSyntenic stdin droYak2.dm2.rbest.net
    # Extract droYak2-ref'd reciprocal best chain:
    netChainSubset droYak2.dm2.rbest.net droYak2.dm2.tBest.chain stdout \
    | chainStitchId stdin droYak2.dm2.rbest.chain
    # Swap to get dm2-ref'd reciprocal best chain:
    chainSwap droYak2.dm2.rbest.chain stdout \
    | chainSort stdin dm2.droYak2.rbest.chain
    # Net those on dm2 to get dm2-ref'd reciprocal best net:
    chainPreNet dm2.droYak2.rbest.chain \
      /cluster/data/{dm2,droYak2}/chrom.sizes stdout \
    | chainNet -minSpace=1 -minScore=0 \
      stdin /cluster/data/{dm2,droYak2}/chrom.sizes stdout /dev/null \
    | netSyntenic stdin dm2.droYak2.rbest.net
    # Compress and clean up.
    rm droYak2.dm2.tBest.chain
    gzip *.rbest.*
    md5sum *.rbest.*.gz > md5sum.txt