Generic

Function: Find specified motif in sequence

Usage: findMotif [options] -motif=<acgt...> sequence

Function: paraSync 1.0paraSync - uses paraFetch to recursively mirror url to given path

Usage: paraSync {options} N R URL outPath

Function: Split text input into files named by column value

Usage: splitFileByColumn source outDir

Function: Convert ESTs so that orientation matches directory of transcription

Usage: estOrient [options] db estTable outPsl

Function: Convert fa file to tab separated file

Usage: faToTab infileName outFileName

Function: Generate .ra format from lines with pipe-separated fields

Usage: linesToRa in.txt out.ra

Function: makeTableList - create/recreate tableList tables (cache of SHOW TABLES)

Usage: makeTableList [assemblies]

Function: Convert XML dump into a fairly normalized relational databasein the form of a directory full of tab-separated files and tablecreation SQL. You'll need to run autoDtd on the XML file first toget the dtd and stats files.

Usage: xmlToSql in.xml in.dtd in.stats outDir

Function: Convert target coverage of net to a bed file.

Usage: netToBed in.net out.bed

Function: Sum columns in a text file.

Usage: addCols <fileName>

Function: Check for biggest gap in coverage for a list of tracks.For most tracks coverage of 10,000,000 or more will indicate that there wasa mistake in generating the track.

Usage: checkCoverageGaps database track1 ... trackN

Function: Check to see if a twobit file has any identical sequences in it

Usage: twoBitDup file.2bit

Function: hubCheck - Check a track data hub for integrity.

Usage: hubCheck http://yourHost/yourDir/hub.txt

Function: Make binary version of chromGraph.

Usage: chromGraphToBin in.tab out.chromGraph

Function: Validate PSL files

Usage: pslCheck fileTbl(s)