Generic

bedIntersect
Function: Intersect two bed files
Usage: bedIntersect a.bed b.bed output.bed
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
qacToWig
Function: Convert from compressed quality score format to wiggle format.
Usage: qacToWig in.qac outFileOrDir
pslLiftSubrangeBlat
Function: Lift PSLs from blat subrange alignments
Usage: pslLiftSubrangeBlat isPsl outPsl
qacAgpLift
Function: Use AGP to combine per-scaffold qac into per-chrom qac.
Usage: qacAgpLift scaffoldToChrom.agp scaffolds.qac chrom.qac
netToAxt
Function: Convert net (and chain) to axt.
Usage: netToAxt in.net in.chain target.2bit query.2bit out.axt
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
raToTab
Function: Convert ra file to table.
Usage: raToTab in.ra out.tab
ixIxx
Function: Create indices for simple line-oriented file of format<symbol> <free text>
Usage: ixIxx in.text out.ix out.ixx
pslToBed
Function: pslToBed: tranform a psl format file to a bed format file.
Usage: pslToBed psl bed
toUpper
Function: Convert lower case to upper case in file. Leave other chars alone
Usage: toUpper inFile outFile
chainMergeSort
Function: Combine sorted files into larger sorted file
Usage: chainMergeSort file(s)
sizeof
Function: Show size of various C types for reference
Usage: sizeof
bigBedInfo
Function: Show information about a bigBed file.
Usage: bigBedInfo file.bb