gtf2bed

Convert GTF files from, e.g., GENCODE, into a slightly-augmented BED format for use with Dalliance.

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.

To make bigbed files for use with Dalliance, you'll probably want the JKSrc tools from UCSC, or at least a recent version of bedToBigBed.

Converting genes

	java -jar target/gtf2bed-0.0.1-SNAPSHOT-standalone.jar gencode.gtf >gencode.bed

Making bigbed files for Dalliance

	bedToBigBed -type=bed12+4 -as=gencode.as -extraIndex=name gencode.bed hg19.chromInfo gencode.bb

Making gene-name index

            cut -f 4,14 gencode.bed >gencode.txt
            ixIxx gencode.txt gencode.ix gencode.ixx

Note that you need to keep both the .ix and .ixx files.

Configuring a source in Dalliance

                  {name: 'Genes',
                   desc: 'Gene structures from GENCODE 19',
                   bwgURI: 'http://www.biodalliance.org/datasets/gencode19.bb',
                   stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode.xml',
                   collapseSuperGroups: true,
                   trixURI: 'http://www.biodalliance.org/datasets/genecode19.ix'}