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bigWigMerge bigWigMerge in1.bw in2.bw .. inN.bw out.bedGraph bigWigMerge - Merge together multiple bigWigs into a single output bedGraph.You'll have to run bedGraphToBigWig to make the output bigWig.The signal values are just added together to merge them Show
bigBedToBed bigBedToBed input.bb output.bed bigBedToBed - Convert from bigBed to ascii bed format. Show
faSomeRecords faSomeRecords in.fa listFile out.fa faSomeRecords - Extract multiple fa records Show
gff3ToGenePred gff3ToGenePred inGff3 outGp gff3ToGenePred - convert a GFF3 file to a genePred file Show
mafSplit mafSplit splits.bed outRoot file(s).maf mafSplit - Split multiple alignment files Show
wigCorrelate wigCorrelate one.wig two.wig ... n.wig wigCorrelate - Produce a table that correlates all pairs of wigs. Show
genePredToGtf genePredToGtf database genePredTable output.gtf genePredToGtf - Convert genePred table or file to gtf. Show
mafsInRegion mafsInRegion regions.bed out.maf|outDir in.maf(s) mafsInRegion - Extract MAFS in a genomic region Show
bedRemoveOverlap bedRemoveOverlap in.bed out.bed bedRemoveOverlap - Remove overlapping records from a (sorted) bed file. Gets rid of`the smaller of overlapping records. Show
bigWigToBedGraph bigWigToBedGraph in.bigWig out.bedGraph bigWigToBedGraph - Convert from bigWig to bedGraph format. Show
rowsToCols rowsToCols in.txt out.txt rowsToCols - Convert rows to columns and vice versa in a text file. Show
twoBitToFa twoBitToFa input.2bit output.fa twoBitToFa - Convert all or part of .2bit file to fasta Show
mafOrder mafOrder mafIn order.lst mafOut mafOrder - order components within a maf file Show
mafSpeciesSubset mafSpeciesSubset in.maf species.lst out.maf mafSpeciesSubset - Extract a maf that just has a subset of species. Show
bedGraphToBigWig bedGraphToBigWig in.bedGraph chrom.sizes out.bw bedGraphToBigWig v 4 - Convert a bedGraph file to bigWig format. Show
twoBitMask twoBitMask input.2bit maskFile output.2bit twoBitMask - apply masking to a .2bit file, creating a new .2bit file Show
mafToPsl mafToPsl querySrc targetSrc in.maf out.psl mafToPsl - Convert maf to psl format Show
gtfToGenePred gtfToGenePred gtf genePred gtfToGenePred - convert a GTF file to a genePred Show
chainNet chainNet in.chain target.sizes query.sizes target.net query.net chainNet - Make alignment nets out of chains Show
axtChain axtChain -linearGap=loose in.axt tNibDir qNibDir out.chain axtChain - Chain together axt alignments. Show