Software Usage Function
axtSort axtSort in.axt out.axt Sort axt files
calc calc this + that * theOther / (a + b) Little command line calculator
pslMap pslMap [options] inPsl mapFile outPsl Map PSLs alignments to new targets using alignments ofthe old target to the new target. Given inPsl and mapPsl, wherethe target of inPsl is the query of mapPsl, create a new PSLwith the query of inPsl aligned to all the targets of mapPsl.If inPsl is a protein to nucleotide alignment and mapPsl is anucleotide to nucleotide alignment, the resulting alignment isnucleotide to nucleotide alignment of a hypothetical mRNA thatwould code for the protein. This is useful as it gives basealignments of spliced codons. A chain file may be used insteadmapPsl.
pslToChain pslToChain pslIn chainOut Convert psl records to chain records
countChars countChars char file(s) Count the number of occurences of a particular char
faToFastq faToFastq in.fa out.fastq Convert fa to fastq format, just faking quality values.
htmlCheck htmlCheck how url htmlCheck - Do a little reading and verification of html file
overlapSelect overlapSelect [options] selectFile inFile outFile Select records based on overlapping chromosome ranges
pslCat pslCat file(s) Concatenate psl files
pslPretty pslPretty in.psl target.lst query.lst pretty.out Convert PSL to human readable output
checkTableCoords checkTableCoords database [tableName] Check invariants on genomic coords in table(s).
chainSort chainSort inFile outFile Sort chains. By default sorts by score.Note this loads all chains into memory, so it is notsuitable for large sets. Instead, run chainSort onmultiple small files, followed by chainMergeSort.
gapToLift gapToLift [options] db liftFile.lft Create lift file from gap table(s)
nibSize nibSize nib1 [...] Print size of nibs
tailLines tailLines file tail Add tail to each line of file
pslSort pslSort dirs[1|2] outFile tempDir inDir(s) Merge and sort psCluster .psl output files
bedToPsl bedToPsl chromSizes bedFile pslFile Convert bed format files to psl format
chromGraphFromBin chromGraphFromBin in.chromGraph Convert chromGraph binary to ascii format.
faNoise faNoise inName outName transitionPpt transversionPpt insertPpt deletePpt chimeraPpt Add noise to fasta file
bedSort bedSort in.bed out.bed Sort a bed file by chromosome name and start position