Generic

Function: Merge multiple regions in BED 5 filesgenerated by liftOver -multiple

Usage: liftOverMerge oldFile newFile

Function: Convert rows to columns and vice versa in a text file (transpose)

Usage: rowsToCols in.txt out.txt

Function: Chain together axt alignments.

Usage: axtChain -linearGap=loose in.axt tNibDir qNibDir out.chain

Function: Convert bed format files to genePred format

Usage: bedToGenePred bedFile genePredFile

Function: Filter chain files. Output goes to standard out.

Usage: chainFilter file(s)

Function: Filter fasta records, selecting ones that match the specified conditions

Usage: faFilter [options] in.fa out.fa

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

Function: Extend length of entries in bed 6+ data to be at least the given length, taking strand directionality into account.

Usage: bedExtendRanges database length files(s)

Function: Convert chain file to psl format

Usage: chainToPsl in.chain tSizes qSizes target.lst query.lst out.psl

Function: Apply masking to a .2bit file, creating a new .2bit file

Usage: twoBitMask input.2bit maskFile output.2bit

Function: Load database with gene predictions from a gff file.

Usage: ldHgGene database table file(s).gff

Function: Make alignment nets out of chains

Usage: chainNet in.chain target.sizes query.sizes target.net query.net

Function: Filter cDNA alignments in psl format

Usage: pslCDnaFilter [options] inPsl outPsl

Function: catUncomment - Concatenate input removing lines that start with '#'Output goes to stdout

Usage: catUncomment file(s)

Function: catDir - concatenate files in directory to stdout.For those times when too many files for cat to handle.

Usage: catDir dir(s)