Software Usage Function
faOneRecord faOneRecord in.fa recordName Extract a single record from a fasta file
twoBitInfo twoBitInfo input.2bit Get information about sequences in a .2bit file
faCmp faCmp [options] a.fa b.fa Compare two fasta files
netSyntenic netSyntenic Add synteny info to net.
pslReps pslReps in.psl out.psl out.psr Analyse repeats and generate genome wide bestalignments from a sorted set of local alignments
bigWigToWig bigWigToWig in.bigWig out.wig 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.
genePredSingleCover genePredSingleCover [options] inGenePred outGenePred Create single-coverage genePred files
colTransform colTransform column addFactor mulFactor colTransform - Add and/or multiply column by constant.
netClass netClass [options] tDb qDb Add classification info to net
crTreeSearchBed crTreeSearchBed file.bed chrom start end Search a crTree indexed bed file and print all items that overlap query.
hgFindSpec hgFindSpec [options] orgDir database hgFindSpec hgFindSpec.sql hgRoot Create hgFindSpec table from trackDb.ra files.
maskOutFa maskOutFa in.fa maskFile out.fa.masked Produce a masked .fa file given an unmasked .fa anda RepeatMasker .out file, or a .bed file to mask on.
wigEncode wigEncode [options] wigInput wigFile wibFile Convert Wiggle ascii data to binary format
checkHgFindSpec checkHgFindSpec database [options | termToSearch] Test and describe search specs in hgFindSpec tables.
nibFrag nibFrag [options] file.nib start end strand out.fa Extract part of a nib file as .fa (all bases/gaps lower case by default)
splitFile splitFile source linesPerFile outBaseName Split up a file
chainPreNet chainPreNet in.chain target.sizes query.sizes out.chain Remove chains that don't have a chance of being netted
headRest headRest count fileName Return all *but* the first N lines of a file.
chopFaLines chopFaLines in.fa out.fa Read in FA file with long lines and rewrite it with shorter lines
chainSplit chainSplit outDir inChain(s) Split chains up by target or query sequence