This directory contains reciprocal-best netted chains for dm2-droSim1.

 - dm2.droSim1.rbest.net.gz: dm2-referenced recip.best net to droSim1.
 - dm2ToDroSim1.rbest.over.chain.gz: chains extracted from the recip.best 
   net -- these can be passed to the liftOver program to translate coords 
   from dm2 to droSim1 through the recip.best net.

 - droSim1.dm2.rbest.net.gz: droSim1-referenced recip.best net.
 - droSim1ToDm2.rbest.over.chain.gz: recip.best "liftOver" chains.

Here is how these files were generated, starting with the file 
dm2.droSim1.all.chain.gz which can be downloaded from ../ 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.  

    # Run chainNet again, this time keeping its second output:
    chainPreNet dm2.droSim1.all.chain.gz \
      /cluster/data/{dm2,droSim1}/chrom.sizes stdout \
    | chainNet stdin /cluster/data/{dm2,droSim1}/chrom.sizes /dev/null stdout \
    | netSyntenic stdin droSim1.dm2_ref.net
    # Get the droSim1 chains from the droSim1-referenced (but dm2-centric) net:
    chainSwap dm2.droSim1.all.chain.gz droSim1.dm2.all.chain
    netChainSubset droSim1.dm2_ref.net droSim1.dm2.all.chain stdout \
    | chainSort stdin droSim1.dm2_ref.subset.chain
    # Net those (sorted) D.mel. chains, and keep both outputs, to get 
    # reciprocal best nets referenced to both species:
    chainPreNet droSim1.dm2_ref.subset.chain \
      /cluster/data/{droSim1,dm2}/chrom.sizes stdout \
    | chainNet stdin /cluster/data/{droSim1,dm2}/chrom.sizes \
      tmp1 tmp2
    netSyntenic tmp1 droSim1.dm2.rbest.net
    netSyntenic tmp2 dm2.droSim1.rbest.net
    rm tmp1 tmp2
    # Get the chains from the recip-best nets for stringent liftOver:
    netChainSubset droSim1.dm2.rbest.net droSim1.dm2.all.chain \
      droSim1ToDm2.rbest.over.chain
    netChainSubset dm2.droSim1.rbest.net dm2.droSim1.all.chain.gz \
      dm2ToDroSim1.rbest.over.chain
    nice gzip droSim1* dm2.droSim1.rbest.net dm2ToDroSim1.rbest.over.chain

      Name                             Last modified      Size  Description
      Parent Directory                                      -   
      dm2.droSim1.rbest.net.gz         2006-02-28 15:32  502K  
      droSim1.dm2.rbest.net.gz         2006-02-28 15:32  873K  
      dm2ToDroSim1.rbest.over.chain.gz 2006-02-28 15:34  2.2M  
      droSim1ToDm2.rbest.over.chain.gz 2006-02-28 15:34  2.7M