Generic

axtChain
Function: Chain together axt alignments.
Usage: axtChain -linearGap=loose in.axt tNibDir qNibDir out.chain
bedToGenePred
Function: Convert bed format files to genePred format
Usage: bedToGenePred bedFile genePredFile
faToTwoBit
Function: Convert DNA from fasta to 2bit format
Usage: faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit
ldHgGene
Function: Load database with gene predictions from a gff file.
Usage: ldHgGene database table file(s).gff
bigWigToWig
Function: Convert bigWig to wig. This will keep more of the same structure of theoriginal wig than bigWigToBedGraph does, but still will break up large stepped sectionsinto smaller ones.
Usage: bigWigToWig in.bigWig out.wig
liftOverMerge
Function: Merge multiple regions in BED 5 filesgenerated by liftOver -multiple
Usage: liftOverMerge oldFile newFile
rowsToCols
Function: Convert rows to columns and vice versa in a text file (transpose)
Usage: rowsToCols in.txt out.txt
chainFilter
Function: Filter chain files. Output goes to standard out.
Usage: chainFilter file(s)
chainStitchId
Function: 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.
Usage: chainStitchId in.chain out.chain
chainNet
Function: Make alignment nets out of chains
Usage: chainNet in.chain target.sizes query.sizes target.net query.net
chainToPsl
Function: Convert chain file to psl format
Usage: chainToPsl in.chain tSizes qSizes target.lst query.lst out.psl
twoBitMask
Function: Apply masking to a .2bit file, creating a new .2bit file
Usage: twoBitMask input.2bit maskFile output.2bit
twoBitInfo
Function: Get information about sequences in a .2bit file
Usage: twoBitInfo input.2bit output.tab
netSyntenic
Function: Add synteny info to net.
Usage: netSyntenic in.net out.net
pslCDnaFilter
Function: Filter cDNA alignments in psl format
Usage: pslCDnaFilter [options] inPsl outPsl