Software Usage Function
blastXmlToPsl blastXmlToPsl [options] blastXml psl Convert blast XML output to PSLs
pslFilter pslFilter in.psl out.psl Filter out psl file
pslSwap pslSwap [options] inPsl outPsl Swap target and query in psls -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output -r hg19.refseq.bed12 Calculate inner distance between read pairs.
crTreeIndexBed crTreeIndexBed in.bed Create an index for a bed file.
featureBits featureBits database table(s) Correlate tables via bitmap projections.
axtToPsl axtToPsl in.axt tSizes qSizes out.psl Convert axt to psl format
bigBedNamedItems bigBedNamedItems name output.bed Extract item of given name from bigBed
chainSwap chainSwap in.chain out.chain Swap target and query in chain
makeTableList makeTableList [assemblies] makeTableList - create/recreate tableList tables (cache of SHOW TABLES)
twoBitDup twoBitDup file.2bit Check to see if a twobit file has any identical sequences in it
pslPairs creates: <outFilePrefix>.pairs file Join paired ends in psl alignments
axtSwap axtSwap source.axt target.sizes query.sizes dest.axt Swap source and query in an axt file
pslRecalcMatch pslRecalcMatch in.psl targetSeq querySeq out.psl Recalculate match,mismatch,repMatch columns in psl file.This can be useful if the psl went through pslMap, or if you've addedlower-case repeat masking after the fact
chromGraphToBin chromGraphToBin out.chromGraph Make binary version of chromGraph.
xmlToSql xmlToSql in.xml in.dtd in.stats outDir 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.
pslCheck pslCheck fileTbl(s) Validate PSL files
spacedToTab spacedToTab in.txt Convert fixed width space separated fields to tab separatedNote this requires two passes, so it can't be done on a pipe
bedWeedOverlapping bedWeedOverlapping weeds.bed input.bed output.bed Filter out beds that overlap a 'weed.bed' file.
checkCoverageGaps checkCoverageGaps database track1 ... trackN 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.