Software Usage Function
faFilterN faFilterN in.fa out.fa maxPercentN Get rid of sequences with too many N's
checkAgpAndFa checkAgpAndFa in.agp in.fa Take a .agp file and .fa file and ensure that they are in synch
localtime localtime Convert unix timestamp to date string
faTrans faTrans in.fa out.fa Translate DNA .fa file to peptide
bedItemOverlapCount sort bedFile.bed | bedItemOverlapCount [options] <database> stdin Count number of times a base is overlapped by theitems in a bed file. Output is bedGraph 4 to stdout.
faSize faSize file(s).fa Print total base count in fa files.
mrnaToGene mrnaToGene [options] psl genePredFile Convert PSL alignments of mRNAs to gene annotations
chainToAxt chainToAxt in.chain tNibDirOr2bit qNibDirOr2bit out.axt Convert from chain to axt file
pslPartition pslPartition [options] pslFile outDircreated under outDir to prevent slow access to huge directories. Split PSL files into non-overlapping sets
sqlToXml sqlToXml database dumpSpec.od output.xml Dump out all or part of a relational database to XML, guidedby a dump specification. See sqlToXml.doc for additional information.
faToTwoBit faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit Convert DNA from fasta to 2bit format nr90.clstr nr60.clstr > nr60_from90.clstr It combines a .clstr file with its parent .clstr file
faFrag faFrag in.fa start end out.fa Extract a piece of DNA from a fasta file.
pslLiftSubrangeBlat pslLiftSubrangeBlat isPsl outPsl Lift PSLs from blat subrange alignments
qacToWig qacToWig in.qac outFileOrDir Convert from compressed quality score format to wiggle format.
bedIntersect bedIntersect a.bed b.bed output.bed Intersect two bed files
dbSnoop dbSnoop database output Produce an overview of a database.
qaToQac qaToQac out.qac Convert from uncompressed to compressedquality score format.
bedClip bedClip input.bed chrom.sizes output.bed Remove lines from bed file that refer to off-chromosome places.
qacAgpLift qacAgpLift scaffoldToChrom.agp scaffolds.qac chrom.qac Use AGP to combine per-scaffold qac into per-chrom qac.