Software Usage Function
bigWigMerge bigWigMerge .. out.bedGraph Merge together multiple bigWigs into a single output bedGraph.
bigBedToBed bigBedToBed output.bed Convert from bigBed to ascii bed format.
gff3ToGenePred gff3ToGenePred inGff3 outGp Convert a GFF3 file to a genePred file
bedGraphToBigWig bedGraphToBigWig in.bedGraph chrom.sizes Convert a bedGraph file to bigWig format.
bigWigToBedGraph bigWigToBedGraph in.bigWig out.bedGraph Convert from bigWig to bedGraph format.
genePredToGtf genePredToGtf database genePredTable output.gtf Convert genePred table or file to gtf.
genePredToBed genePredToBed in.genePred out.bed Convert from genePred to bed format
lavToAxt lavToAxt in.lav tNibDir qNibDir out.axt Convert blastz lav file to an axt file (which includes sequence)
wiggletools wiggletools sum [bigwig files...] Merge BigWig files