GenometriCorr USCS examples

We used two BED files in examples, both are generated by USCS genome bioinformatics browser.

The coords of USCS CpG islands were retrieved by http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&command=start&db=hg19&hgta_database=hg19&hgta_fieldSelectTable=hg19.cpgIslandExt&hgta_fs.check.hg19.cpgIslandExt.chrom=1&hgta_fs.check.hg19.cpgIslandExt.chromEnd=1&hgta_fs.check.hg19.cpgIslandExt.chromStart=1>a_fs.check.hg19.cpgIslandExt.cpgNum=0&hgta_fs.check.hg19.cpgIslandExt.gcNum=0&hgta_fs.check.hg19.cpgIslandExt.length=0&hgta_fs.check.hg19.cpgIslandExt.name=0&hgta_fs.check.hg19.cpgIslandExt.obsExp=0&hgta_fs.check.hg19.cpgIslandExt.perCpg=0&hgta_fs.check.hg19.cpgIslandExt.perGc=0&hgta_group=regulation&hgta_outputType=primaryTable&hgta_regionType=genome&hgta_table=cpgIslandExt&hgta_track=cpgIslandExt&hgta_doPrintSelectedFields=&org=Human&.

The coords of RefSeq genes were retrieved by http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_database=hg19&hgta_group=genes&hgta_track=refGene&hgta_table=refGene&hgta_regionType=genome&hgta_outputType=primaryTable&hgta_fieldSelectTable=hg19.refGene&hgta_fs.check.hg19.refGene.chrom=1&hgta_fs.check.hg19.refGene.name=0&hgta_fs.check.hg19.refGene.txEnd=1&hgta_fs.check.hg19.refGene.txStart=1&hgta_doPrintSelectedFields=&.

Creation of such URLs is described here GenomeWiki and here DigitHead's lab notebook.

The chromosome length data was extracted from the UCSC hg19 chromosome information table.