Software Usage Function
hgTrackDb hgTrackDb [options] org database trackDb trackDb.sql hgRoot Create trackDb table from text files.Note that the browser supports multiple trackDb tables, usuallyin the form: trackDb_YourUserName. Which particular trackDbtable the browser uses is specified in the hg.conf file foundeither in your home directory file '.hg.conf' or in the web server'scgi-bin/hg.conf configuration file with the setting: db.trackDb=trackDbsee also: src/product/ex.hg.conf discussion of this setting.
lavToPsl lavToPsl in.lav out.psl Convert blastz lav to psl format
raSqlQuery raSqlQuery raFile(s) query-options Do a SQL-like query on a RA file
netToBed netToBed out.bed Convert target coverage of net to a bed file.
bedRestrictToPositions bedRestrictToPositions in.bed restrict.bed out.bed Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file.
qacToQa qacToQa in.qac Convert from compressed to uncompressedquality score format.
hgLoadBed hgLoadBed database track files(s).bed Load a generic bed file into database
addCols addCols <fileName> Sum columns in a text file.
bedPileUps bedPileUps in.bed Find (exact) overlaps if any in bed input
faRc faRc in.fa out.fa Reverse complement a FA file
splitFileByColumn splitFileByColumn source outDir Split text input into files named by column value
faToTab faToTab infileName outFileName Convert fa file to tab separated file
hubCheck hubCheck http://yourHost/yourDir/hub.txt hubCheck - Check a track data hub for integrity.
paraSync paraSync {options} N R URL outPath paraSync 1.0paraSync - uses paraFetch to recursively mirror url to given path
estOrient estOrient [options] db estTable outPsl Convert ESTs so that orientation matches directory of transcription
linesToRa linesToRa in.txt out.ra Generate .ra format from lines with pipe-separated fields
pslSelect pslSelect [options] inPsl outPsl Select records from a PSL file.
subColumn subColumn column Substitute one column in a tab-separated file.
cd-hit-div cd-hit-div -i input -o output -div n Divide a FASTA file into pieces
liftUp liftUp [] destFile liftSpec how sourceFile(s) Change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf.bscore .tab .gdup .axt .chain .net, genePred, .wab, .bed, or .bed8 files toparent coordinate system.