Generic

Function: Find specified motif in sequence

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

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

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

Function: Validate PSL files

Usage: pslCheck fileTbl(s)

Function: Swap target and query in psls

Usage: pslSwap [options] inPsl outPsl

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: Swap source and query in an axt file

Usage: axtSwap source.axt target.sizes query.sizes dest.axt

Function: Create an index for a bed file.

Usage: crTreeIndexBed in.bed out.cr

Function: Filter out beds that overlap a 'weed.bed' file.

Usage: bedWeedOverlapping weeds.bed input.bed output.bed

Function: Average together columns

Usage: aveCols file

Function: Convert pslx (with sequence) to fasta file

Usage: pslxToFa in.psl out.fa

Function: Create SQL and C code for permanently storinga structure in database and loading it back into memorybased on a specification file

Usage: autoSql specFile outRoot {optional: -dbLink -withNull -json}

Function: Join paired ends in psl alignments

Usage: creates: <outFilePrefix>.pairs file

Function: positionalTblCheck - check that positional tables are sorted

Usage: positionalTblCheck db table

Function: Output .ra file stanzas as single lines, with pipe-separated fields.

Usage: raToLines in.ra out.txt

Function: Convert fixed width space separated fields to tab separatedNote this requires two passes, so it can't be done on a pipe

Usage: spacedToTab in.txt out.tab