hubbub

Tools for preparing track-hub-style datasets.

Building

Install Leiningen then:

  lein deps
  lein uberjar

Compiled jar files will end up in the target directory. If you use the -standalone jar file, there shouldn't be any other requirements to run it.

Converting over.chain files to bigBed

    java -cp target/hubbub-0.0.1-SNAPSHOT-standalone.jar \
       hubbub.tools.chain2bed hg18ToHg19.over.chain >hg18ToHg19.bed
    sort -k1,1 -k2,2n hg18ToHg19.bed >hg18ToHg19.sorted.bed
    bedToBigBed -type=bed3+9 -as=as/chain.as hg18ToHg19.sorted.bed chrom.sizes hg18ToHg19.bb