Generic

netToAxt
Function: Convert net (and chain) to axt.
Usage: netToAxt in.net in.chain target.2bit query.2bit out.axt
clstr_rev.pl
Function: It combines a .clstr file with its parent .clstr file
Usage: clstr_rev.pl nr90.clstr nr60.clstr > nr60_from90.clstr
mrnaToGene
Function: Convert PSL alignments of mRNAs to gene annotations
Usage: mrnaToGene [options] psl genePredFile
bedIntersect
Function: Intersect two bed files
Usage: bedIntersect a.bed b.bed output.bed
bigBedInfo
Function: Show information about a bigBed file.
Usage: bigBedInfo file.bb
qacToWig
Function: Convert from compressed quality score format to wiggle format.
Usage: qacToWig in.qac outFileOrDir
autoXml
Function: Generate structures code and parser for XML file from DTD-like spec
Usage: autoXml file.dtdx root
tdbQuery
Function: Query the trackDb system using SQL syntax.
Usage: tdbQuery sqlStatement
tickToDate
Function: Convert seconds since 1970 to time and date
Usage: tickToDate ticks
ixIxx
Function: Create indices for simple line-oriented file of format<symbol> <free text>
Usage: ixIxx in.text out.ix out.ixx
qaToQac
Function: Convert from uncompressed to compressedquality score format.
Usage: qaToQac in.qa out.qac
hgLoadOut
Function: Load RepeatMasker .out files into database
Usage: hgLoadOut database file(s).out
qacAgpLift
Function: Use AGP to combine per-scaffold qac into per-chrom qac.
Usage: qacAgpLift scaffoldToChrom.agp scaffolds.qac chrom.qac
samtools flags
Function: Convert between textual and numeric flag representation.
Usage: samtools flags INT|STR[,...]
faRandomize
Function: Program to create random fasta records
Usage: faRandomize [-seed=N] in.fa randomized.fa