Software Usage Function
wigCorrelate wigCorrelate one.wig two.wig ... n.wig Produce a table that correlates all pairs of wigs
mafsInRegion mafsInRegion regions.bed out.maf|outDir in.maf(s) mafsInRegion - Extract MAFS in a genomic region
bedRemoveOverlap bedRemoveOverlap in.bed out.bed bedRemoveOverlap - Remove overlapping records from a (sorted) bed file. Gets rid of`the smaller of overlapping records.
twoBitToFa twoBitToFa input.2bit output.fa Convert all or part of .2bit file to fasta
gtfToGenePred gtfToGenePred gtf genePred gtfToGenePred - convert a GTF file to a genePred
liftOverMerge liftOverMerge oldFile newFile liftOverMerge - Merge multiple regions in BED 5 filesgenerated by liftOver -multiple
mafSpeciesSubset mafSpeciesSubset in.maf species.lst out.maf mafSpeciesSubset - Extract a maf that just has a subset of species.
rowsToCols rowsToCols in.txt out.txt rowsToCols - Convert rows to columns and vice versa in a text file.
mafToPsl mafToPsl querySrc targetSrc in.maf out.psl mafToPsl - Convert maf to psl format
axtChain axtChain -linearGap=loose in.axt tNibDir qNibDir out.chain axtChain - Chain together axt alignments.
mafOrder mafOrder mafIn order.lst mafOut mafOrder - order components within a maf file
chainFilter chainFilter file(s) chainFilter - Filter chain files. Output goes to standard out.
bigBedSummary bigBedSummary chrom start end dataPoints bigBedSummary - Extract summary information from a bigBed file.
faFilter faFilter [options] in.fa out.fa faFilter - Filter fa records, selecting ones that match the specified conditions
chainStitchId chainStitchId in.chain out.chain chainStitchId - Join chain fragments with the same chain ID into a singlechain per ID. Chain fragments must be from same original chain butmust not overlap. Chain fragment scores are summed.
bedExtendRanges bedExtendRanges database length files(s) bedExtendRanges - extend length of entries in bed 6+ data to be at least the given length,taking strand directionality into account.
twoBitMask twoBitMask input.2bit maskFile output.2bit twoBitMask - apply masking to a .2bit file, creating a new .2bit file
bedToGenePred bedToGenePred bedFile genePredFile Too few arguments:bedToGenePred - convert bed format files to genePred format
bigWigAverageOverBed bigWigAverageOverBed in.bed bigWigAverageOverBed - Compute average score of big wig over each bed, which may have introns.
chainToPsl chainToPsl in.chain tSizes qSizes target.lst query.lst out.psl chainToPsl - Convert chain file to psl format