Software Usage Function
samtools flags samtools flags INT|STR[,...] Convert between textual and numeric flag representation.
faRandomize faRandomize [-seed=N] in.fa randomized.fa Program to create random fasta records
ixIxx ixIxx in.text out.ix out.ixx Create indices for simple line-oriented file of format<symbol> <free text>
pslToBed pslToBed psl bed pslToBed: tranform a psl format file to a bed format file.
raToTab raToTab in.ra Convert ra file to table.
gmtime gmtime Convert unix timestamp to date string
autoXml autoXml file.dtdx root Generate structures code and parser for XML file from DTD-like spec
bigBedInfo bigBedInfo Show information about a bigBed file.
netSplit netSplit outDir Split a genome net file into chromosome net files
bedGeneParts bedGeneParts part in.bed out.bed Given a bed, spit out promoter, first exon, or all introns.
hgGcPercent hgGcPercent [options] database nibDir Calculate GC Percentage in 20kb windows
paraFetch paraFetch N R URL {outPath} Try to fetch url with multiple connections
genePredCheck genePredCheck [options] fileTbl .. Validate genePred files or tables
rmFaDups rmFaDup oldName.fa newName.fa Remove duplicate records in FA file
sizeof sizeof Show size of various C types for reference
textHistogram textHistogram [options] inFile Make a histogram in ascii
samtools dict samtools dict <ref.fasta|ref.fasta.gz> Create a sequence dictionary file from a fasta file.
dbTrash dbTrash -age=N [-drop] [-historyToo] [-db=<DB>] [-verbose=N] Drop tables from a database older than specified N hours
genePredHisto genePredHisto [options] what genePredFile histoOut Get data for generating histograms from a genePred file.
gff3ToPsl gff3ToPsl mapFile inGff3 out.psl Convert a GFF3 CIGAR file to a PSL file