Generic

Function: Intersect two bed files

Usage: bedIntersect a.bed b.bed output.bed

Function: It combines a .clstr file with its parent .clstr file

Usage: clstr_rev.pl nr90.clstr nr60.clstr > nr60_from90.clstr

Function: Convert from compressed quality score format to wiggle format.

Usage: qacToWig in.qac outFileOrDir

Function: Lift PSLs from blat subrange alignments

Usage: pslLiftSubrangeBlat isPsl outPsl

Function: Use AGP to combine per-scaffold qac into per-chrom qac.

Usage: qacAgpLift scaffoldToChrom.agp scaffolds.qac chrom.qac

Function: Convert net (and chain) to axt.

Usage: netToAxt in.net in.chain target.2bit query.2bit out.axt

Function: Convert from uncompressed to compressedquality score format.

Usage: qaToQac in.qa out.qac

Function: Load RepeatMasker .out files into database

Usage: hgLoadOut database file(s).out

Function: Convert ra file to table.

Usage: raToTab in.ra out.tab

Function: Create indices for simple line-oriented file of format<symbol> <free text>

Usage: ixIxx in.text out.ix out.ixx

Function: pslToBed: tranform a psl format file to a bed format file.

Usage: pslToBed psl bed

Function: Convert lower case to upper case in file. Leave other chars alone

Usage: toUpper inFile outFile

Function: Combine sorted files into larger sorted file

Usage: chainMergeSort file(s)

Function: Show size of various C types for reference

Usage: sizeof

Function: Show information about a bigBed file.

Usage: bigBedInfo file.bb