Kent source utilities: Difference between revisions

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<TABLE>
The list that used to be on this page is outdated. Please see the current list here:
<TR><TD ALIGN=LEFT>aNotB:</TD><TD>List symbols that are in a but not b</TD></TR>
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER
<TR><TD ALIGN=LEFT>addAveMedScoreToPsls:</TD><TD>Combines unigene pslFile and sage file into bed file</TD></TR>
<TR><TD ALIGN=LEFT>addCols:</TD><TD>Sum columns in a text file.</TD></TR>
<TR><TD ALIGN=LEFT>affyPairsToSample:</TD><TD>Takes a 'pairs' format file from the Affy transcriptome
data set and combines it with the Affy offset.txt file to output a 'sample' file
which has the contig coordinates of the result.</TD></TR>
<TR><TD ALIGN=LEFT>agpAllToFaFile:</TD><TD>Convert all sequences in an .agp file to a .fa file </TD></TR>


<TR><TD ALIGN=LEFT>agpCloneCheck:</TD><TD>Check that have all clones in an agp file (and the right version too)</TD></TR>
[[Category:Technical FAQ]]
<TR><TD ALIGN=LEFT>agpCloneList:</TD><TD>Make simple list of all clones in agp file
to stdout</TD></TR>
<TR><TD ALIGN=LEFT>agpToFa:</TD><TD>Convert a .agp file to a .fa file</TD></TR>
<TR><TD ALIGN=LEFT>agpToGl:</TD><TD>Convert AGP file to GL file.  Some fakery involved.</TD></TR>
<TR><TD ALIGN=LEFT>agxToIntronBeds:</TD><TD>Program to output all introns from altGraphX
records as beds. Designed for use in MGC project looking for novel
introns from altGraphX records transferred over from mouse.</TD></TR>
<TR><TD ALIGN=LEFT>ali2alx:</TD><TD>produces an index file for each chromosome into an ali file.</TD></TR>
 
<TR><TD ALIGN=LEFT>aliGlue:</TD><TD>tell where a cDNA is located quickly.</TD></TR>
<TR><TD ALIGN=LEFT>ameme:</TD><TD>find common patterns in DNA
usage
    ameme good=goodIn.fa [bad=badIn.fa] [numMotifs=2] [background=m1] [maxOcc=2] [motifOutput=fileName] [html=output.html] [gif=output.gif] [rcToo=on] [controlRun=on] [startScanLimit=20] [outputLogo] [constrainer=1]</TD></TR>
<TR><TD ALIGN=LEFT>assessLibs:</TD><TD>Make table that assesses the percentage of library that covers 5' and 3' ends</TD></TR>
<TR><TD ALIGN=LEFT>autoDtd:</TD><TD>Give this a XML document to look at and it will come up with a DTD
to describe it.</TD></TR>
<TR><TD ALIGN=LEFT>autoSql:</TD><TD>create SQL and C code for permanently storing
a structure in database and loading it back into memory
based on a specification file</TD></TR>
<TR><TD ALIGN=LEFT>autoXml:</TD><TD>Generate structures code and parser for XML file from DTD-like spec</TD></TR>
 
<TR><TD ALIGN=LEFT>ave:</TD><TD>Compute average and basic stats</TD></TR>
<TR><TD ALIGN=LEFT>aveCols:</TD><TD>average together columns</TD></TR>
<TR><TD ALIGN=LEFT>averagExp:</TD><TD>Average expression data within a cluster</TD></TR>
<TR><TD ALIGN=LEFT>averageZoomLevels:</TD><TD>takes a sorted sample file and creates averaged
'zoomed-out' summaries for a few different levels.
Basic idea is to get the size of a chromosome, divide it by 2000 as that is</TD></TR>
<TR><TD ALIGN=LEFT>avgTranscriptomeExps:</TD><TD>Averages together replicates of the affy transcriptome data set.
Will skip certain experiments unless directed otherwise as they
were not in the original data set.</TD></TR>
<TR><TD ALIGN=LEFT>axtAndBed:</TD><TD>Intersect an axt with a bed file and output axt.</TD></TR>
 
<TR><TD ALIGN=LEFT>axtBest:</TD><TD>Remove second best alignments</TD></TR>
<TR><TD ALIGN=LEFT>axtCalcMatrix:</TD><TD>Calculate substitution matrix and make indel histogram</TD></TR>
<TR><TD ALIGN=LEFT>axtChain:</TD><TD>Chain together axt alignments.</TD></TR>
<TR><TD ALIGN=LEFT>axtDropOverlap:</TD><TD>deletes all overlapping self alignments. </TD></TR>
<TR><TD ALIGN=LEFT>axtDropSelf:</TD><TD>Drop alignments that just align same thing to itself</TD></TR>
<TR><TD ALIGN=LEFT>axtFilter:</TD><TD>Filter axt files.  Output goes to standard out.</TD></TR>
 
<TR><TD ALIGN=LEFT>axtForEst:</TD><TD>Generate file of mouse/human alignments corresponding to MGC EST's</TD></TR>
<TR><TD ALIGN=LEFT>axtIndex:</TD><TD>build index of axt file</TD></TR>
<TR><TD ALIGN=LEFT>axtPretty:</TD><TD>Convert axt to more human readable format.</TD></TR>
<TR><TD ALIGN=LEFT>axtQueryCount:</TD><TD>Count bases covered on each query sequence</TD></TR>
<TR><TD ALIGN=LEFT>axtRecipBest:</TD><TD>create file for dot plot using recip best </TD></TR>
<TR><TD ALIGN=LEFT>axtRescore:</TD><TD>Recalculate scores in axt.</TD></TR>
 
<TR><TD ALIGN=LEFT>axtSort:</TD><TD>Sort axt files</TD></TR>
<TR><TD ALIGN=LEFT>axtSplitByTarget:</TD><TD>Split a single axt file into one file per target</TD></TR>
<TR><TD ALIGN=LEFT>axtSwap:</TD><TD>Swap source and query in an axt file</TD></TR>
<TR><TD ALIGN=LEFT>axtToBed:</TD><TD>Convert axt alignments to simple bed format</TD></TR>
<TR><TD ALIGN=LEFT>axtToChain:</TD><TD>Convert axt to chain format</TD></TR>
<TR><TD ALIGN=LEFT>axtToMaf:</TD><TD>Convert from axt to maf format</TD></TR>
 
<TR><TD ALIGN=LEFT>axtToPsl:</TD><TD>Convert axt to psl format</TD></TR>
<TR><TD ALIGN=LEFT>bedCons:</TD><TD>Look at conservation of a BED track vs. a refence (nonredundant) alignment track</TD></TR>
<TR><TD ALIGN=LEFT>bedCoverage:</TD><TD>Analyse coverage by bed files - chromosome by
chromosome and genome-wide.</TD></TR>
<TR><TD ALIGN=LEFT>bedDown:</TD><TD>Make stuff to find a BED format submission in a new version</TD></TR>
<TR><TD ALIGN=LEFT>bedIntersect:</TD><TD>Intersect two bed files</TD></TR>
<TR><TD ALIGN=LEFT>bedItemOverlapCount:</TD><TD>count number of times a base is overlapped by the
items in a bed file.  Output is bedGraph 4 to stdout.</TD></TR>
 
<TR><TD ALIGN=LEFT>bedSort:</TD><TD>Sort a .bed file by chrom,chromStart</TD></TR>
<TR><TD ALIGN=LEFT>bedToFrames:</TD><TD>Makes html files for browsing custom bed track
using frames. Use -pad for padding</TD></TR>
<TR><TD ALIGN=LEFT>bedToGenePred:</TD><TD>Too few arguments:
convert bed format files to genePred format</TD></TR>
<TR><TD ALIGN=LEFT>bedUp:</TD><TD>Load bed submissions after conversion back into new database.</TD></TR>
<TR><TD ALIGN=LEFT>binGood:</TD><TD>convert text format alignment file to binary format</TD></TR>
<TR><TD ALIGN=LEFT>blastToPsl:</TD><TD>Convert blast alignments to PSLs.</TD></TR>
 
<TR><TD ALIGN=LEFT>blat:</TD><TD>Standalone BLAT v. 33x3 fast sequence search command line tool</TD></TR>
<TR><TD ALIGN=LEFT>blatz:</TD><TD>blatz version 1 - Align dna across species</TD></TR>
<TR><TD ALIGN=LEFT>blatzClient:</TD><TD>blatzClient version 1 - Ask server to do
cross-species DNA alignments and save results.</TD></TR>
<TR><TD ALIGN=LEFT>blatzServer:</TD><TD>blatzServer version 1 - Set up in-memory server for
cross-species DNA alignments</TD></TR>
<TR><TD ALIGN=LEFT>borfBig:</TD><TD>Run Victor Solovyev's bestorf repeatedly</TD></TR>
<TR><TD ALIGN=LEFT>bwana:</TD><TD>do batch coarse alignment of C. briggsae and C. elegans genomes.</TD></TR>
 
<TR><TD ALIGN=LEFT>calc:</TD><TD>Little command line calculator</TD></TR>
<TR><TD ALIGN=LEFT>calcGap:</TD><TD>calculate gap scores</TD></TR>
<TR><TD ALIGN=LEFT>catDir:</TD><TD>concatenate files in directory to stdout.
For those times when too many files for cat to handle.</TD></TR>
<TR><TD ALIGN=LEFT>catUncomment:</TD><TD>Concatenate input removing lines that start with '#'
Output goes to stdout</TD></TR>
<TR><TD ALIGN=LEFT>ccCp:</TD><TD>copy a file to cluster.usage:
  ccCp sourceFile destFile [hostList]
This will copy sourceFile to destFile for all machines in</TD></TR>
<TR><TD ALIGN=LEFT>cdnaOff:</TD><TD>creates sorted offset files that position cDNAs in chromosome.</TD></TR>
 
<TR><TD ALIGN=LEFT>chainAntiRepeat:</TD><TD>Get rid of chains that are primarily the results of repeats and degenerate DNA</TD></TR>
<TR><TD ALIGN=LEFT>chainDbToFile:</TD><TD>translate a chain's db representation back to file</TD></TR>
<TR><TD ALIGN=LEFT>chainFilter:</TD><TD>Filter chain files.  Output goes to standard out.</TD></TR>
<TR><TD ALIGN=LEFT>chainMergeSort:</TD><TD>Combine sorted files into larger sorted file</TD></TR>
<TR><TD ALIGN=LEFT>chainNet:</TD><TD>Make alignment nets out of chains</TD></TR>
<TR><TD ALIGN=LEFT>chainPreNet:</TD><TD>Remove chains that don't have a chance of being netted</TD></TR>
 
<TR><TD ALIGN=LEFT>chainSort:</TD><TD>Sort chains.  By default sorts by score.
Note this loads all chains into memory, so it is not
suitable for large sets.  Use chainMergeSort for that</TD></TR>
<TR><TD ALIGN=LEFT>chainSplit:</TD><TD>Split chains up by target or query sequence</TD></TR>
<TR><TD ALIGN=LEFT>chainStats:</TD><TD>Stitch psls into chains</TD></TR>
<TR><TD ALIGN=LEFT>chainSwap:</TD><TD>Swap target and query in chain</TD></TR>
<TR><TD ALIGN=LEFT>chainToPsl:</TD><TD>Convert chain file to psl format</TD></TR>
<TR><TD ALIGN=LEFT>checkAgpAndFa:</TD><TD>takes a .agp file and .fa file and ensures that they are in synch</TD></TR>
 
<TR><TD ALIGN=LEFT>checkHgFindSpec:</TD><TD>test and describe search specs in hgFindSpec tables.</TD></TR>
<TR><TD ALIGN=LEFT>checkTableCoords:</TD><TD>check invariants on genomic coords in table(s).</TD></TR>
<TR><TD ALIGN=LEFT>checkableBorf:</TD><TD>Convert borfBig orf-finder output to checkable form</TD></TR>
<TR><TD ALIGN=LEFT>chopFaLines:</TD><TD>Read in FA file with long lines and rewrite it with shorter lines</TD></TR>
<TR><TD ALIGN=LEFT>cluster:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>clusterGenes:</TD><TD>Cluster genes from genePred tracks</TD></TR>
 
<TR><TD ALIGN=LEFT>clusterRna:</TD><TD>Make clusters of mRNA and ESTs</TD></TR>
<TR><TD ALIGN=LEFT>convolve:</TD><TD>perform convolution of probabilities</TD></TR>
<TR><TD ALIGN=LEFT>countChars:</TD><TD>Count the number of occurences of a particular char</TD></TR>
<TR><TD ALIGN=LEFT>createSageSummary:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>ctgFaToFa:</TD><TD>Convert from one big file with all NT contigs to one contig per file.</TD></TR>
<TR><TD ALIGN=LEFT>ctgToChromFa:</TD><TD>convert contig level fa files to chromosome level</TD></TR>
 
<TR><TD ALIGN=LEFT>dbSnoop:</TD><TD>Produce an overview of a database.</TD></TR>
<TR><TD ALIGN=LEFT>detab:</TD><TD>remove tabs from program</TD></TR>
<TR><TD ALIGN=LEFT>dnaMotifFind:</TD><TD>Locate preexisting motifs in DNA sequence</TD></TR>
<TR><TD ALIGN=LEFT>eisenInput:</TD><TD>Create input for Eisen-style cluster program</TD></TR>
<TR><TD ALIGN=LEFT>emblMatrixToMotif:</TD><TD>Convert transfac matrix in EMBL format to dnaMotif</TD></TR>
<TR><TD ALIGN=LEFT>embossToPsl:</TD><TD>Convert EMBOSS pair alignments to PSL format</TD></TR>
 
<TR><TD ALIGN=LEFT>endsInLf:</TD><TD>Check that last letter in files is end of line</TD></TR>
<TR><TD ALIGN=LEFT>est2genomeToPsl:</TD><TD>Convert EMBOSS est2genome and WUSTL pairgon alignments to
PSL format</TD></TR>
<TR><TD ALIGN=LEFT>estLibStats:</TD><TD>Calculate some stats on EST libraries given file from polyInfo</TD></TR>
<TR><TD ALIGN=LEFT>estOrient:</TD><TD>estOrient [options] db estTable outPsl</TD></TR>
<TR><TD ALIGN=LEFT>exonAli:</TD><TD>This program aligns cDNA with genomic sequence. Usage:
    exonAli named output cdnaName(s)
    exonAli in output listFile</TD></TR>
<TR><TD ALIGN=LEFT>expToRna:</TD><TD>Make a little two column table that associates
rnaClusters with expression info</TD></TR>
 
<TR><TD ALIGN=LEFT>faAlign:</TD><TD>Align two fasta files</TD></TR>
<TR><TD ALIGN=LEFT>faCmp:</TD><TD>Compare two .fa files</TD></TR>
<TR><TD ALIGN=LEFT>faCount:</TD><TD>count base statistics and CpGs in FA files.</TD></TR>
<TR><TD ALIGN=LEFT>faFilter:</TD><TD>Filter fa records, selecting ones that match the specified conditions</TD></TR>
<TR><TD ALIGN=LEFT>faFilterN:</TD><TD>Get rid of sequences with too many N's</TD></TR>
<TR><TD ALIGN=LEFT>faFlyBaseToUcsc:</TD><TD>Convert Flybase peptide fasta file to UCSC format</TD></TR>
 
<TR><TD ALIGN=LEFT>faFrag:</TD><TD>Extract a piece of DNA from a .fa file.</TD></TR>
<TR><TD ALIGN=LEFT>faGapSizes:</TD><TD>report on gap size counts/statistics</TD></TR>
<TR><TD ALIGN=LEFT>faNcbiToUcsc:</TD><TD>Convert FA file from NCBI to UCSC format.</TD></TR>
<TR><TD ALIGN=LEFT>faNoise:</TD><TD>Add noise to .fa file</TD></TR>
<TR><TD ALIGN=LEFT>faOneRecord:</TD><TD>Extract a single record from a .FA file</TD></TR>
<TR><TD ALIGN=LEFT>faPolyASizes:</TD><TD>get poly A sizes</TD></TR>
 
<TR><TD ALIGN=LEFT>faRc:</TD><TD>Reverse complement a FA file</TD></TR>
<TR><TD ALIGN=LEFT>faSimplify:</TD><TD>Simplify fasta record headers</TD></TR>
<TR><TD ALIGN=LEFT>faSize:</TD><TD>print total base count in fa files.</TD></TR>
<TR><TD ALIGN=LEFT>faSomeRecords:</TD><TD>Extract multiple fa records</TD></TR>
<TR><TD ALIGN=LEFT>faSplit:</TD><TD>Split an fa file into several files.</TD></TR>
<TR><TD ALIGN=LEFT>faToNib:</TD><TD>Convert from .fa to .nib format</TD></TR>
 
<TR><TD ALIGN=LEFT>faToTab:</TD><TD>hgFaToTab - convert fa file to tab separted file</TD></TR>
<TR><TD ALIGN=LEFT>faToTwoBit:</TD><TD>Convert DNA from fasta to 2bit format</TD></TR>
<TR><TD ALIGN=LEFT>faTrans:</TD><TD>Translate DNA .fa file to peptide</TD></TR>
<TR><TD ALIGN=LEFT>faTrimPolyA:</TD><TD>trim poly-A tails</TD></TR>
<TR><TD ALIGN=LEFT>faTrimRead:</TD><TD>trim reads based on qual scores - change low scoring bases to N's </TD></TR>
<TR><TD ALIGN=LEFT>fakeFinContigs:</TD><TD>Fake up contigs for a finished chromosome</TD></TR>
 
<TR><TD ALIGN=LEFT>fakeOut:</TD><TD>fake a RepeatMasker .out file based on a N's in .fa file</TD></TR>
<TR><TD ALIGN=LEFT>fatont4:</TD><TD>fato4nt - a program to convert .fa files to .4nt files</TD></TR>
<TR><TD ALIGN=LEFT>featureBits:</TD><TD>Correlate tables via bitmap projections. </TD></TR>
<TR><TD ALIGN=LEFT>ffaToFa:</TD><TD>ffaToFa convert Greg Schuler .ffa fasta files to UCSC .fa fasta files</TD></TR>
<TR><TD ALIGN=LEFT>findCdna:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>findMotif:</TD><TD>find specified motif in sequence</TD></TR>
 
<TR><TD ALIGN=LEFT>findStanAlignments:</TD><TD>takes a stanford microarray experiment file and
tries to look up an alignment for the relevant clone in the database.
Starts by trying to look up the longest genbank clone from image id, </TD></TR>
<TR><TD ALIGN=LEFT>fishClones:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>fixCr:</TD><TD>strip <CR>s from ends of lines</TD></TR>
<TR><TD ALIGN=LEFT>fixcr:</TD><TD>removes trailing carraige returns from files.</TD></TR>
<TR><TD ALIGN=LEFT>fqToQa:</TD><TD>convert from fq format with one big file to
format with one file per clone.</TD></TR>
<TR><TD ALIGN=LEFT>fqToQac:</TD><TD>convert from fq format with one big file to
compressed format with one file per clone.</TD></TR>
 
<TR><TD ALIGN=LEFT>fragPart:</TD><TD>get part of a fragment's sequence</TD></TR>
<TR><TD ALIGN=LEFT>gb2cdi:</TD><TD>convert GeneBank (GB) files to .fa and cDna Info (CDI) file.</TD></TR>
<TR><TD ALIGN=LEFT>gbGetEntries:</TD><TD>retrieve records from a GenBank flat file.</TD></TR>
<TR><TD ALIGN=LEFT>gbOneAcc:</TD><TD>retrieve one or a few records from a GenBank flat file.</TD></TR>
<TR><TD ALIGN=LEFT>gbToFaRa:</TD><TD>Convert GenBank flat format file to an fa file containing
the sequence data, an ra file containing other relevant info and
a ta file containing summary statistics.</TD></TR>
<TR><TD ALIGN=LEFT>gbtofa:</TD><TD>gbtofa converts from GeneBank to fa format.</TD></TR>
 
<TR><TD ALIGN=LEFT>gcForBed:</TD><TD>Calculate g/c percentage and other stats for regions covered by bed</TD></TR>
<TR><TD ALIGN=LEFT>genePredCheck:</TD><TD>validate genePred files or tables</TD></TR>
<TR><TD ALIGN=LEFT>genePredHisto:</TD><TD>wrong number of arguments
get data for generating histograms from a genePred file.</TD></TR>
<TR><TD ALIGN=LEFT>genePredSingleCover:</TD><TD>wrong # args
create single-coverage genePred files</TD></TR>
<TR><TD ALIGN=LEFT>genePredToFakePsl:</TD><TD>Create a psl of fake-mRNA aligned to gene-preds from a file or table.</TD></TR>
<TR><TD ALIGN=LEFT>genePredToGtf:</TD><TD>Convert genePred table or file to gtf.</TD></TR>
 
<TR><TD ALIGN=LEFT>genePredToMafFrames:</TD><TD>wrong # args
create mafFrames tables from a genePreds</TD></TR>
<TR><TD ALIGN=LEFT>geniegff:</TD><TD>makes up a gdf file from Genie gene predictions</TD></TR>
<TR><TD ALIGN=LEFT>getFeatDna:</TD><TD>Get dna for a type of feature</TD></TR>
<TR><TD ALIGN=LEFT>getRna:</TD><TD>Get mrna for GenBank or RefSeq sequences found in a database</TD></TR>
<TR><TD ALIGN=LEFT>getRnaPred:</TD><TD>Get virtual RNA for gene predictions</TD></TR>
<TR><TD ALIGN=LEFT>gfClient:</TD><TD>gfClient v. 33x3 - A client for the genomic finding program that produces a .psl file</TD></TR>
 
<TR><TD ALIGN=LEFT>gfPcr:</TD><TD>In silico PCR version 33x3 using gfServer index.</TD></TR>
<TR><TD ALIGN=LEFT>gfServer:</TD><TD>gfServer v 33x3 - Make a server to quickly find where DNA occurs in genome.
To set up a server:
  gfServer start host port file(s)</TD></TR>
<TR><TD ALIGN=LEFT>gffPeek:</TD><TD>Look at a gff file and report some basic stats</TD></TR>
<TR><TD ALIGN=LEFT>gffgenes:</TD><TD>creates files that store extents of genes for intronerator</TD></TR>
<TR><TD ALIGN=LEFT>gpStats:</TD><TD>Figure out some stats on the golden path.</TD></TR>
<TR><TD ALIGN=LEFT>gpToGtf:</TD><TD>Convert gp table to GTF</TD></TR>
 
<TR><TD ALIGN=LEFT>gpcrParser:</TD><TD>Create xml files for gpcr snakeplots.</TD></TR>
<TR><TD ALIGN=LEFT>groupSamples:</TD><TD>Group samples together into one sample.
Samples must be sorted by chromosome position (you can
use bedSort first if they are not).</TD></TR>
<TR><TD ALIGN=LEFT>gsBig:</TD><TD>Run Genscan on big input and produce GTF files and other parsed output</TD></TR>
<TR><TD ALIGN=LEFT>gtfToGenePred:</TD><TD>convert a GTF file to a genePred</TD></TR>
<TR><TD ALIGN=LEFT>headRest:</TD><TD>Return all *but* the first N lines of a file.</TD></TR>
<TR><TD ALIGN=LEFT>hgAddLiftOverChain:</TD><TD>Add a liftOver chain to the central database</TD></TR>
 
<TR><TD ALIGN=LEFT>hgAvidShortBed:</TD><TD>Convert short form of AVID alignments to BED</TD></TR>
<TR><TD ALIGN=LEFT>hgBioCyc:</TD><TD>bioCyc - Creates bioCycPathway.tab for Known Genes to link to SRI BioCyc pathways</TD></TR>
<TR><TD ALIGN=LEFT>hgCeOrfToGene:</TD><TD>Make orfToGene table for C.elegans from GENE_DUMPS/gene_names.txt</TD></TR>
<TR><TD ALIGN=LEFT>hgChroms:</TD><TD>print chromosomes for a genome.</TD></TR>
<TR><TD ALIGN=LEFT>hgClonePos:</TD><TD>create clonePos table in browser database</TD></TR>
<TR><TD ALIGN=LEFT>hgClusterGenes:</TD><TD>Cluster overlapping gene predictions</TD></TR>
 
<TR><TD ALIGN=LEFT>hgCountAlign:</TD><TD>count overlaping or non-overlaping windows in an alignment.</TD></TR>
<TR><TD ALIGN=LEFT>hgCtgPos:</TD><TD>Store contig positions ( from lift files ) in database.</TD></TR>
<TR><TD ALIGN=LEFT>hgDeleteChrom:</TD><TD>output SQL commands to delete a chrom from the database</TD></TR>
<TR><TD ALIGN=LEFT>hgEmblProtLinks:</TD><TD>Parse EMBL flat file into protein link table</TD></TR>
<TR><TD ALIGN=LEFT>hgExonerate:</TD><TD>Convert Exonerate modified GFF files to BED format and load in database.</TD></TR>
<TR><TD ALIGN=LEFT>hgExpDistance:</TD><TD>Create table that measures expression distance between pairs</TD></TR>
 
<TR><TD ALIGN=LEFT>hgExperiment:</TD><TD>Load data from a BED of region positions,
            an experiment file containing <name> [<description>]</TD></TR>
<TR><TD ALIGN=LEFT>hgExtFileCheck:</TD><TD>check extFile or gbExtFile tables against file system</TD></TR>
<TR><TD ALIGN=LEFT>hgFakeAgp:</TD><TD>Create fake AGP file by looking at N's</TD></TR>
<TR><TD ALIGN=LEFT>hgFiberglass:</TD><TD>Turn Fiberglass Annotations into a BED and load into database</TD></TR>
<TR><TD ALIGN=LEFT>hgFindSpec:</TD><TD>Create hgFindSpec table from trackDb.ra files.</TD></TR>
 
<TR><TD ALIGN=LEFT>hgFlyBase:</TD><TD>Parse FlyBase genes.txt file and turn it into a couple of tables</TD></TR>
<TR><TD ALIGN=LEFT>hgGcPercent:</TD><TD>Calculate GC Percentage in 20kb windows</TD></TR>
<TR><TD ALIGN=LEFT>hgGeneBands:</TD><TD>Find bands for all genes</TD></TR>
<TR><TD ALIGN=LEFT>hgGetAnn:</TD><TD>get chromosome annotation rows from database tables using
          browser-style position specification.</TD></TR>
<TR><TD ALIGN=LEFT>hgGnfMicroarray:</TD><TD>Load data from (2003-style) GNF Affy Microarrays</TD></TR>
<TR><TD ALIGN=LEFT>hgGoAssociation:</TD><TD>Load bits we care about in GO association table</TD></TR>
 
<TR><TD ALIGN=LEFT>hgGoldGapGl:</TD><TD>Put chromosome .agp and .gl files into browser database.</TD></TR>
<TR><TD ALIGN=LEFT>hgKegg:</TD><TD>creates keggPathway.tab and keggMapDesc.tab files for KG links to KEGG Pathway Mapusage:
  hgKegg xxxx
      xxxx is the genome database name</TD></TR>
<TR><TD ALIGN=LEFT>hgKegg2:</TD><TD>creates keggPathway.tab and keggMapDesc.tab files for KG links to KEGG Pathway Mapusage:
  hgKegg2 kgTempDb roDb
      kgTempDb is the KG build temp database name</TD></TR>
<TR><TD ALIGN=LEFT>hgKgGetText:</TD><TD>Get text from known genes into a file.
The file will be line oriented with the known gene ID as
the first word, and the rest of the word being a conglomaration</TD></TR>
<TR><TD ALIGN=LEFT>hgKgMrna:</TD><TD>Load mRNA alignments and other info into refGene tables
          into a TEMPORARY database to build Known Genes track.</TD></TR>
<TR><TD ALIGN=LEFT>hgKnownMore:</TD><TD>Create the knownMore table from a variety of sources.</TD></TR>
 
<TR><TD ALIGN=LEFT>hgKnownToSuper:</TD><TD>Load knownToSuperfamily table</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadBed:</TD><TD>Load a generic bed file into database</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadBlastTab:</TD><TD>Load blast table into database</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadChain:</TD><TD>Load a generic Chain file into database</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadGap:</TD><TD>Load gap table from AGP-style file containing only gaps</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadGenePred:</TD><TD>wrong # args
Load up a mySQL database genePred table</TD></TR>
 
<TR><TD ALIGN=LEFT>hgLoadItemAttr:</TD><TD>load an itemAttr table</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadMaf:</TD><TD>Load a maf file index into the database</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadMafFrames:</TD><TD>wrong # args
load an mafFrames table</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadMafSummary:</TD><TD>Load a summary table of pairs in a maf into a database</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadNet:</TD><TD>Load a generic net file into database</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadOut:</TD><TD>load RepeatMasker .out files into database</TD></TR>
 
<TR><TD ALIGN=LEFT>hgLoadPsl:</TD><TD>Load up a mySQL database with psl alignment tables</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadSample:</TD><TD>Load a sample 9 (wiggle) file into database</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadSeq:</TD><TD>load browser database with sequence file info.</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadSqlTab:</TD><TD>Load table into database from SQL and text files.</TD></TR>
<TR><TD ALIGN=LEFT>hgLoadWiggle:</TD><TD>Load a wiggle track definition into database</TD></TR>
<TR><TD ALIGN=LEFT>hgMapMicroarray:</TD><TD>Make mapped version of microarray data, merging psl in.</TD></TR>
 
<TR><TD ALIGN=LEFT>hgMapToGene:</TD><TD>Map a track to a genePred track.</TD></TR>
<TR><TD ALIGN=LEFT>hgMapViaSwissProt:</TD><TD>Make table that maps to external database via SwissProt</TD></TR>
<TR><TD ALIGN=LEFT>hgMedianMicroarray:</TD><TD>Create a copy of microarray database that contains the
median value of replicas</TD></TR>
<TR><TD ALIGN=LEFT>hgMrnaRefseq:</TD><TD>creates xref data between mRNAand RefSeq from LocusLink data contained in 2 tables from a temporary DBusage:
  hgMrnaRefseq xxxx
      xxxx is the genome database name</TD></TR>
<TR><TD ALIGN=LEFT>hgNearTest:</TD><TD>Test hgNear web page</TD></TR>
<TR><TD ALIGN=LEFT>hgNetDist:</TD><TD>GS loader for gene/protein interaction network distances.</TD></TR>
 
<TR><TD ALIGN=LEFT>hgNibSeq:</TD><TD>convert DNA to nibble-a-base and store location in database</TD></TR>
<TR><TD ALIGN=LEFT>hgPepPred:</TD><TD>Load peptide predictions from Ensembl or Genie</TD></TR>
<TR><TD ALIGN=LEFT>hgPhMouse:</TD><TD>Load phMouse track</TD></TR>
<TR><TD ALIGN=LEFT>hgProtIdToGenePred:</TD><TD>Add proteinID column to genePrediction</TD></TR>
<TR><TD ALIGN=LEFT>hgRatioMicroarray:</TD><TD>Create a ratio form of microarray data.</TD></TR>
<TR><TD ALIGN=LEFT>hgRnaGenes:</TD><TD>Turn RNA genes from GFF into database format (BED variant)</TD></TR>
 
<TR><TD ALIGN=LEFT>hgSanger20:</TD><TD>Load extra info from Sanger Chromosome 20 annotations.</TD></TR>
<TR><TD ALIGN=LEFT>hgSanger22:</TD><TD>Load up database with Sanger 22 annotations</TD></TR>
<TR><TD ALIGN=LEFT>hgSoftPromoter:</TD><TD>Slap Softberry promoter file into database.</TD></TR>
<TR><TD ALIGN=LEFT>hgSoftberryHom:</TD><TD>Make table storing Softberry protein homology information</TD></TR>
<TR><TD ALIGN=LEFT>hgSpeciesRna:</TD><TD>Create fasta file with RNA from one species</TD></TR>
<TR><TD ALIGN=LEFT>hgStanfordMicroarray:</TD><TD>Load up from Stanford Microarray Database files</TD></TR>
 
<TR><TD ALIGN=LEFT>hgStsAlias:</TD><TD>Make table of STS aliases</TD></TR>
<TR><TD ALIGN=LEFT>hgStsMarkers:</TD><TD>Load STS markers into database</TD></TR>
<TR><TD ALIGN=LEFT>hgTablesTest:</TD><TD>Test hgTables web page</TD></TR>
<TR><TD ALIGN=LEFT>hgTpf:</TD><TD>Make TPF table</TD></TR>
<TR><TD ALIGN=LEFT>hgTraceInfo:</TD><TD>import subset of mouse trace ancillary information
parsed from FASTA files</TD></TR>
<TR><TD ALIGN=LEFT>hgTrackDb:</TD><TD>Create trackDb table from text files.
Note that the browser supports multiple trackDb tables, usually</TD></TR>
 
<TR><TD ALIGN=LEFT>hgWaba:</TD><TD>load Waba alignments into database</TD></TR>
<TR><TD ALIGN=LEFT>hgWiggle:</TD><TD>fetch wiggle data from data base or file</TD></TR>
<TR><TD ALIGN=LEFT>hgWormLinks:</TD><TD>Create table that links worm ORF name to description
and SwissProt.  This works on a WormBase dump, in Ace format
I believe, from Lincoln Stein.</TD></TR>
<TR><TD ALIGN=LEFT>hgsql:</TD><TD>Execute some sql code using passwords in .hg.conf</TD></TR>
<TR><TD ALIGN=LEFT>hgsqladmin:</TD><TD>Wrapper around mysqladmin using passwords in .hg.conf</TD></TR>
<TR><TD ALIGN=LEFT>hgsqldump:</TD><TD>Execute mysqldump using passwords from .hg.conf</TD></TR>
 
<TR><TD ALIGN=LEFT>hgsqlimport:</TD><TD>Execute mysqlimport using passwords from .hg.conf</TD></TR>
<TR><TD ALIGN=LEFT>htmlCheck:</TD><TD>Do a little reading and verification of html file</TD></TR>
<TR><TD ALIGN=LEFT>htmlPics:</TD><TD>create an html file from a list of pictures
usage
    htmlPics picFile(s)</TD></TR>
<TR><TD ALIGN=LEFT>indexfa:</TD><TD>This program makes an index file for a .fa file</TD></TR>
<TR><TD ALIGN=LEFT>indexgl:</TD><TD>This program makes an index file for a .gl file</TD></TR>
<TR><TD ALIGN=LEFT>intronEnds:</TD><TD>Gather stats on intron ends.</TD></TR>
 
<TR><TD ALIGN=LEFT>introns:</TD><TD>Introns - finds the introns in a file and writes them to gff.</TD></TR>
<TR><TD ALIGN=LEFT>iriToControlTable:</TD><TD>Convert improbizer run to simple list of control scores</TD></TR>
<TR><TD ALIGN=LEFT>iriToDnaMotif:</TD><TD>Convert improbRunInfo to dnaMotif</TD></TR>
<TR><TD ALIGN=LEFT>isPcr:</TD><TD>Standalone v 33x3 In-Situ PCR Program</TD></TR>
<TR><TD ALIGN=LEFT>ixIxx:</TD><TD>Create indices for simple line-oriented file of format
<symbol> <free text></TD></TR>
<TR><TD ALIGN=LEFT>ixali:</TD><TD>This program makes a name index file for an .ali file</TD></TR>
 
<TR><TD ALIGN=LEFT>ixword1:</TD><TD>This program makes an index file for text file,
indexing the first word of each line.</TD></TR>
<TR><TD ALIGN=LEFT>ixword3:</TD><TD>This program makes an index file for text file,
indexing the third word of each line.</TD></TR>
<TR><TD ALIGN=LEFT>jkUniq:</TD><TD>remove duplicate lines from file.  Lines need not
be next to each other (plain Unix uniq works for that)</TD></TR>
<TR><TD ALIGN=LEFT>joinableFields:</TD><TD>Return list of good join targets for a table</TD></TR>
<TR><TD ALIGN=LEFT>joinerCheck:</TD><TD>Parse and check joiner file</TD></TR>
<TR><TD ALIGN=LEFT>jp2Info:</TD><TD></TD></TR>
 
<TR><TD ALIGN=LEFT>jp2ToJpg:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>jp2ToJpgTiles:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>kgAliasKgXref:</TD><TD>create gene alias .tab file usage:
  kgAliasKgXref xxxx
            xxxx is genome database name</TD></TR>
<TR><TD ALIGN=LEFT>kgAliasM:</TD><TD>create gene alias (mRNA part) .tab files usage:
  kgAliasM xxxx yyyy
            xxxx is genome  database name</TD></TR>
<TR><TD ALIGN=LEFT>kgAliasP:</TD><TD>create gene alias (protein part) .tab files usage:
  kgAliasM xxxx yyyy zzzz
            xxxx is genome  database name</TD></TR>
<TR><TD ALIGN=LEFT>kgAliasRefseq:</TD><TD>create gene alias .tab file usage:
  kgAliasRefseq xxxx
            xxxx is genome database name</TD></TR>
<TR><TD ALIGN=LEFT>kgCheck:</TD><TD>from gene candidates, go through various criteria and keep the ones that pass the criteria </TD></TR>
 
<TR><TD ALIGN=LEFT>kgGetCds:</TD><TD>create a gene candidate table with CDS info</TD></TR>
<TR><TD ALIGN=LEFT>kgGetPep:</TD><TD>generate FASTA format protein sequence file to be used for Known Genes track build.</TD></TR>
<TR><TD ALIGN=LEFT>kgPepMrna:</TD><TD>generate new .tab files with unused mRNA and protein sequences from known genes db tables removed.usage:
  kgPepMrna tempKgDb roDb YYMMDD
      tempKGDb is the temp KG build database name</TD></TR>
<TR><TD ALIGN=LEFT>kgPick:</TD><TD>select the best repersentative mRNA/protein pair</TD></TR>
<TR><TD ALIGN=LEFT>kgPrepBestMrna2:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>kgPrepBestRef2:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>kgProtAlias:</TD><TD>create protein alias .tab files usage:
  kgProtAlias xxxx yyyy
            xxxx is genome  database name</TD></TR>
 
<TR><TD ALIGN=LEFT>kgProtAliasNCBI:</TD><TD>create gene alias (mRNA part) .tab files usage:
  kgProtAliasNCBI <DB> <RO_DB>
            <DB> is knownGene DB under construction</TD></TR>
<TR><TD ALIGN=LEFT>kgPutBack:</TD><TD>from gene candidates, go through various criteria and keep the ones that pass the criteria </TD></TR>
<TR><TD ALIGN=LEFT>kgResultBestMrna2:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>kgResultBestRef2:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>kgXref:</TD><TD>create Known Gene cross reference table kgXref.tab file.usage:
  kgXref <db> <proteinsYYMMDD> <ro_db>
 
          <db> is known Genes database under construction</TD></TR>
<TR><TD ALIGN=LEFT>kgXref2:</TD><TD>create new Known Gene cross reference table kgXref2.tab file.usage:
  kgXref2 <tmpDb> <YYMMDD> <roDb>
          <tmpDb> is temp KG database under construction</TD></TR>
<TR><TD ALIGN=LEFT>knownVsBlat:</TD><TD>Categorize BLAT mouse hits to known genes</TD></TR>
<TR><TD ALIGN=LEFT>kvsSummary:</TD><TD>Summarize output of a bunch of knownVsBlats</TD></TR>
 
<TR><TD ALIGN=LEFT>lavToAxt:</TD><TD>Convert blastz lav file to an axt file (which includes sequence)</TD></TR>
<TR><TD ALIGN=LEFT>lavToPsl:</TD><TD>Convert blastz lav to psl format</TD></TR>
<TR><TD ALIGN=LEFT>ldHgGene:</TD><TD>load database with gene predictions from a gff file.</TD></TR>
<TR><TD ALIGN=LEFT>lfsOverlap:</TD><TD>remove overlapping records from lfs file and retain the best
scoring lfs record for each set of overlapping records.
If scores are equal, the first record found is retained</TD></TR>
<TR><TD ALIGN=LEFT>libScan:</TD><TD>Scan libraries to help find g' capped ones</TD></TR>
<TR><TD ALIGN=LEFT>liftAgp:</TD><TD> Program to lift tracks that have nearly the same .agp file,
but slightly different. Initially designed for chr21 and chr22 which
are starting to accumulate ticky-tacky changes. Currently works for files</TD></TR>
 
<TR><TD ALIGN=LEFT>liftFrags:</TD><TD>This program lifts annotations on clone fragments
to FPC contig coordinates</TD></TR>
<TR><TD ALIGN=LEFT>liftOver:</TD><TD>Move annotations from one assembly to another</TD></TR>
<TR><TD ALIGN=LEFT>liftOverMerge:</TD><TD>Merge multiple regions in BED 5 files
                  generated by liftOver -multiple</TD></TR>
<TR><TD ALIGN=LEFT>liftPromoHits:</TD><TD>Lift motif hits from promoter to chromosome coordinates</TD></TR>
<TR><TD ALIGN=LEFT>liftUp:</TD><TD>change coordinates of .psl, .agp, .gap, .gl, .out, .gff, .gtf .bscore
.tab .gdup .axt .chain .net, genePred, .wab or .bed files to parent coordinate
system.</TD></TR>
<TR><TD ALIGN=LEFT>lineCount:</TD><TD>Count lines in a file</TD></TR>
 
<TR><TD ALIGN=LEFT>lineFileSplit:</TD><TD>Split up a line oriented file into parts</TD></TR>
<TR><TD ALIGN=LEFT>mafAddIRows:</TD><TD>add 'i' rows to a maf</TD></TR>
<TR><TD ALIGN=LEFT>mafCoverage:</TD><TD>Analyse coverage by maf files - chromosome by
chromosome and genome-wide.</TD></TR>
<TR><TD ALIGN=LEFT>mafFetch:</TD><TD>get overlapping records from an MAF using an index table</TD></TR>
<TR><TD ALIGN=LEFT>mafFilter:</TD><TD>Filter out maf files. Output goes to standard out</TD></TR>
<TR><TD ALIGN=LEFT>mafFrag:</TD><TD>Extract maf sequences for a region from database</TD></TR>
 
<TR><TD ALIGN=LEFT>mafFrags:</TD><TD>Collect MAFs from regions specified in a 6 column bed file</TD></TR>
<TR><TD ALIGN=LEFT>mafOrder:</TD><TD>order components within a maf file</TD></TR>
<TR><TD ALIGN=LEFT>mafRanges:</TD><TD>Extract ranges of target (or query) coverage from maf and
            output as BED 3 (e.g. for processing by featureBits).</TD></TR>
<TR><TD ALIGN=LEFT>mafSplit:</TD><TD>Split multiple alignment files</TD></TR>
<TR><TD ALIGN=LEFT>mafSplitPos:</TD><TD>Pick positions to split multiple alignment input files</TD></TR>
<TR><TD ALIGN=LEFT>mafToAxt:</TD><TD>Convert from maf to axt format</TD></TR>
 
<TR><TD ALIGN=LEFT>mafsInRegion:</TD><TD>Extract MAFS in a genomic region</TD></TR>
<TR><TD ALIGN=LEFT>makeTableDescriptions:</TD><TD>Add table descriptions to database.</TD></TR>
<TR><TD ALIGN=LEFT>makepgo:</TD><TD>Make Predicted Gene Offset files.  One for each chromosome.</TD></TR>
<TR><TD ALIGN=LEFT>maskOutFa:</TD><TD>Produce a masked .fa file given an unmasked .fa and
a RepeatMasker .out file, or a .bed file to mask on.</TD></TR>
<TR><TD ALIGN=LEFT>maxTranscriptomeExps:</TD><TD>cycle through a list of of affy transcriptome
experiments and select the max for each position.</TD></TR>
<TR><TD ALIGN=LEFT>mdToNcbiLift:</TD><TD>Convert seq_contig.md file to ncbi.lft</TD></TR>
 
<TR><TD ALIGN=LEFT>mgcFastaForBed:</TD><TD>Take a bed file and return a fasta file
with exons uppercase and introns lowercase.</TD></TR>
<TR><TD ALIGN=LEFT>mmUnmix:</TD><TD>Help identify human contamination in mouse and vice versa.</TD></TR>
<TR><TD ALIGN=LEFT>moresyn:</TD><TD>find more gene/ORF synonyms</TD></TR>
<TR><TD ALIGN=LEFT>motifLogo:</TD><TD>Make a sequence logo out of a motif.</TD></TR>
<TR><TD ALIGN=LEFT>motifSig:</TD><TD>Combine info from multiple control runs and main improbizer run</TD></TR>
<TR><TD ALIGN=LEFT>mousePoster:</TD><TD>Search database info for making foldout</TD></TR>
 
<TR><TD ALIGN=LEFT>mrnaToGene:</TD><TD>convert PSL alignments of mRNAs to gene annotations</TD></TR>
<TR><TD ALIGN=LEFT>netChainSubset:</TD><TD>Create chain file with subset of chains that appear in the net</TD></TR>
<TR><TD ALIGN=LEFT>netClass:</TD><TD>Add classification info to net</TD></TR>
<TR><TD ALIGN=LEFT>netFilter:</TD><TD>Filter out parts of net.  What passes
filter goes to standard output.  Note a net is a
recursive data structure.  If a parent fails to pass</TD></TR>
<TR><TD ALIGN=LEFT>netSplit:</TD><TD>Split a genome net file into chromosome net files</TD></TR>
<TR><TD ALIGN=LEFT>netStats:</TD><TD>Gather statistics on net</TD></TR>
 
<TR><TD ALIGN=LEFT>netSyntenic:</TD><TD>Add synteny info to net.</TD></TR>
<TR><TD ALIGN=LEFT>netToAxt:</TD><TD>Convert net (and chain) to axt.</TD></TR>
<TR><TD ALIGN=LEFT>netToBed:</TD><TD>Convert target coverage of net to a bed file.</TD></TR>
<TR><TD ALIGN=LEFT>netToBedWithId:</TD><TD>Convert net (and chain) to bed with base identity in score.</TD></TR>
<TR><TD ALIGN=LEFT>newProg:</TD><TD>make a new C source skeleton.</TD></TR>
<TR><TD ALIGN=LEFT>nibFrag:</TD><TD>Extract part of a nib file as .fa (all bases/gaps lower case by default)</TD></TR>
 
<TR><TD ALIGN=LEFT>nibSize:</TD><TD>print size of nibs</TD></TR>
<TR><TD ALIGN=LEFT>normalizeSampleFile:</TD><TD>normalizeSampleFiles - calculates average value over a series of
sample files and sets the average of each sample file to the global
average. Optionally will also group together samples into larger groups.</TD></TR>
<TR><TD ALIGN=LEFT>nt4Frag:</TD><TD>Extract a piece of a .nt4 file to .fa format</TD></TR>
<TR><TD ALIGN=LEFT>orf:</TD><TD>Find orf for cDNAs</TD></TR>
<TR><TD ALIGN=LEFT>orfStats:</TD><TD>Collect stats on orfs</TD></TR>
<TR><TD ALIGN=LEFT>orthoEvaluate:</TD><TD>Evaluate the coding potential of a bed.
  (version: .c,v 1.12 2003/09/14 23:15:02 sugnet )
  -help -- Display this message.</TD></TR>
 
<TR><TD ALIGN=LEFT>orthoMap:</TD><TD>Map items from one organism to another. Must
specify one type of item using the -itemFile or -itemTable
flags. OrthoMap simply maps over the genomic coordinates discarding</TD></TR>
<TR><TD ALIGN=LEFT>orthoPickIntron:</TD><TD>Pick best intron from orthoEval.
  (version: 1.7 2003/09/14 23:15:02 sugnet )
  -help -- Display this message.</TD></TR>
<TR><TD ALIGN=LEFT>orthologBySynteny:</TD><TD>Find syntenic location for a list of gene predictions on a single chromosome</TD></TR>
<TR><TD ALIGN=LEFT>overlapSelect:</TD><TD>wrong # args:  overlapSelect [options] selectFile inFile outFile
Select records based on overlaping chromosome ranges.</TD></TR>
<TR><TD ALIGN=LEFT>patCount:</TD><TD>counts up the number of occurences of each
oligo of a fixed size (up to 13) in input.  Writes out
all patterns that are overrepresented by at least factor</TD></TR>
<TR><TD ALIGN=LEFT>pepPredToFa:</TD><TD>Convert a pepPred table to fasta format</TD></TR>
 
<TR><TD ALIGN=LEFT>pfamXref:</TD><TD>create pfam xref .tab file usage:
  pfamXref pn pfamInput pfamOutput pfamXref
            pn is protein database name</TD></TR>
<TR><TD ALIGN=LEFT>phToPsl:</TD><TD>Convert from Pattern Hunter to PSL format</TD></TR>
<TR><TD ALIGN=LEFT>polyInfo:</TD><TD>Collect info on polyAdenylation signals etc</TD></TR>
<TR><TD ALIGN=LEFT>promoSeqFromCluster:</TD><TD>Get promoter regions from cluster</TD></TR>
<TR><TD ALIGN=LEFT>pslCDnaFilter:</TD><TD>Filter cDNA alignments in psl format.  Filtering criteria are</TD></TR>
<TR><TD ALIGN=LEFT>pslCat:</TD><TD>concatenate psl files</TD></TR>
 
<TR><TD ALIGN=LEFT>pslCheck:</TD><TD>validate PSL files</TD></TR>
<TR><TD ALIGN=LEFT>pslCoverage:</TD><TD>estimate coverage from alignments.usage:
    pslCoverage in.sizes in.psl minPercentId endTrim out.cov misAsm.out</TD></TR>
<TR><TD ALIGN=LEFT>pslDiff:</TD><TD>Compare queries in two or more psl files </TD></TR>
<TR><TD ALIGN=LEFT>pslDropOverlap:</TD><TD>deletes all overlapping self alignments. </TD></TR>
<TR><TD ALIGN=LEFT>pslFilter:</TD><TD>filter out psl file
    pslFilter in.psl out.psl </TD></TR>
<TR><TD ALIGN=LEFT>pslFilterPrimers:</TD><TD></TD></TR>
 
<TR><TD ALIGN=LEFT>pslGlue:</TD><TD>reduce a psl mRNA alignment file to only the components
that might be involved in gluing</TD></TR>
<TR><TD ALIGN=LEFT>pslHisto:</TD><TD>pslHisto [options] what inPsl outHisto</TD></TR>
<TR><TD ALIGN=LEFT>pslHitPercent:</TD><TD>Figure out percentage of reads in FA file that hit.</TD></TR>
<TR><TD ALIGN=LEFT>pslIntronsOnly:</TD><TD>Filter psl files to only include those with introns</TD></TR>
<TR><TD ALIGN=LEFT>pslMap:</TD><TD>map PSLs alignments to new targets using alignments of
the old target to the new target.  Given inPsl and mapPsl, where</TD></TR>
<TR><TD ALIGN=LEFT>pslMrnaCover:</TD><TD>Make histogram of coverage percentage of mRNA in psl.</TD></TR>
 
<TR><TD ALIGN=LEFT>pslPairs:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>pslPartition:</TD><TD>split PSL files into non-overlapping sets</TD></TR>
<TR><TD ALIGN=LEFT>pslPretty:</TD><TD>Convert PSL to human readable output</TD></TR>
<TR><TD ALIGN=LEFT>pslQuickFilter:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>pslRecalcMatch:</TD><TD>Recalculate match,mismatch,repMatch columns in psl file.
This can be useful if the psl went through pslMap, or if you've added
lower-case repeat masking after the fact</TD></TR>
<TR><TD ALIGN=LEFT>pslReps:</TD><TD>analyse repeats and generate genome wide best
alignments from a sorted set of local alignments</TD></TR>
<TR><TD ALIGN=LEFT>pslSelect:</TD><TD>select records from a PSL file.</TD></TR>
 
<TR><TD ALIGN=LEFT>pslSimp:</TD><TD>create simplified version of psl file.</TD></TR>
<TR><TD ALIGN=LEFT>pslSort:</TD><TD>merge and sort psCluster .psl output files</TD></TR>
<TR><TD ALIGN=LEFT>pslSortAcc:</TD><TD>sort pslSort .psl output file by accession
Make one output .psl file per accession.</TD></TR>
<TR><TD ALIGN=LEFT>pslStats:</TD><TD>collect statistics from a psl file.</TD></TR>
<TR><TD ALIGN=LEFT>pslSwap:</TD><TD>wrong # args:
pslSwap [options] inPsl outPsl</TD></TR>
<TR><TD ALIGN=LEFT>pslToBed:</TD><TD>pslToBed: tranform a psl format file to a bed format file.</TD></TR>
 
<TR><TD ALIGN=LEFT>pslToXa:</TD><TD>Convert from psl to xa alignment format</TD></TR>
<TR><TD ALIGN=LEFT>pslUniq:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>pslUnpile:</TD><TD>Removes huge piles of alignments from sorted
psl files (due to unmasked repeats presumably).</TD></TR>
<TR><TD ALIGN=LEFT>pslxToFa:</TD><TD>convert pslx (with sequence) to fasta file</TD></TR>
<TR><TD ALIGN=LEFT>qaToQac:</TD><TD>convert from uncompressed to compressed
quality score format.</TD></TR>
<TR><TD ALIGN=LEFT>qacAgpLift:</TD><TD>Use AGP to combine per-scaffold qac into per-chrom qac.</TD></TR>
 
<TR><TD ALIGN=LEFT>qacToQa:</TD><TD>convert from compressed to uncompressed
quality score format.</TD></TR>
<TR><TD ALIGN=LEFT>qacToWig:</TD><TD>convert from compressed quality score format to wiggle format.</TD></TR>
<TR><TD ALIGN=LEFT>raToCds:</TD><TD>Extract CDS positions from ra file</TD></TR>
<TR><TD ALIGN=LEFT>randomLines:</TD><TD>Pick out random lines from file</TD></TR>
<TR><TD ALIGN=LEFT>randomPlacement:</TD><TD>run placement trials on a set of elements</TD></TR>
<TR><TD ALIGN=LEFT>refiAli:</TD><TD>This program turns rough alignments into fine ones.</TD></TR>
 
<TR><TD ALIGN=LEFT>regionPicker:</TD><TD>Code to pick regions to annotate deeply.
Stratifies genome based on mouse non-transcribed homology
and spliced EST density.</TD></TR>
<TR><TD ALIGN=LEFT>relPairs:</TD><TD>extract pairs from a big pair list file that actually
occur in a .psl file</TD></TR>
<TR><TD ALIGN=LEFT>reviewSanity:</TD><TD>Look through sanity files and make sure things are ok.</TD></TR>
<TR><TD ALIGN=LEFT>rikenBestInCluster:</TD><TD>Find best looking in Riken cluster</TD></TR>
<TR><TD ALIGN=LEFT>rmFaDups:</TD><TD>rmFaDup - remove duplicate records in FA file
usage
  rmFaDup oldName.fa newName.fa</TD></TR>
<TR><TD ALIGN=LEFT>rmKGPepMrna:</TD><TD>generate new .tab files with unused mRNA and protein sequences from known genes db tables removed.usage:
  rmKGPepMrna xxxx yyyy
      xxxx is the genome  database name</TD></TR>
 
<TR><TD ALIGN=LEFT>rowsToCols:</TD><TD>Convert rows to columns and vice versa in a text file.</TD></TR>
<TR><TD ALIGN=LEFT>safePush:</TD><TD>Push database tables from one machine to another. This is a
little more careful than mypush.  It should be run on the machine that is
the source of the data</TD></TR>
<TR><TD ALIGN=LEFT>sanger22gtf:</TD><TD>Convert Sanger chromosome 22 annotations to gtf</TD></TR>
<TR><TD ALIGN=LEFT>scaffoldFaToAgp:</TD><TD>generate an AGP file, gap file, and lift file from a scaffold FA file.</TD></TR>
<TR><TD ALIGN=LEFT>scaleSampleFiles:</TD><TD>scale all of the scores in a file by a scale factor.</TD></TR>
<TR><TD ALIGN=LEFT>scanRa:</TD><TD>scan through ra files for info.</TD></TR>
 
<TR><TD ALIGN=LEFT>scrambleFa:</TD><TD>scramble the order of records in an fa file</TD></TR>
<TR><TD ALIGN=LEFT>selectTrainedHits:</TD><TD>Select only hits from sites that we've trained on</TD></TR>
<TR><TD ALIGN=LEFT>semiNorm:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>sim4big:</TD><TD>A wrapper for Sim4 that runs it repeatedly on a multi-sequence .fa file</TD></TR>
<TR><TD ALIGN=LEFT>simpleChain:</TD><TD>Not supported on x86_64</TD></TR>
<TR><TD ALIGN=LEFT>snpException:</TD><TD>Get exceptions to a snp invariant rule.</TD></TR>
 
<TR><TD ALIGN=LEFT>snpValid:</TD><TD>Validate snp alignments</TD></TR>
<TR><TD ALIGN=LEFT>sortFilt:</TD><TD>merge, sort, and filter patSpace .hit output.</TD></TR>
<TR><TD ALIGN=LEFT>spLoadPsiBlast:</TD><TD>load swissprot PSL-BLAST table.
This loads the results of all-against-all PSI-BLAST on Swissprot, which</TD></TR>
<TR><TD ALIGN=LEFT>spLoadRankProp:</TD><TD>load swissprot rankProp table.</TD></TR>
<TR><TD ALIGN=LEFT>spOrganism:</TD><TD>Extract taxonomy data from SWISS-PROT data file and
produce a .tab file of SWISS-PROT display ID/NCBI taxonomy ID pairs.</TD></TR>
<TR><TD ALIGN=LEFT>spTest:</TD><TD>Test out sp library.</TD></TR>
 
<TR><TD ALIGN=LEFT>spToDb:</TD><TD>Create a relational database out of SwissProt/trEMBL flat files</TD></TR>
<TR><TD ALIGN=LEFT>spToProteins:</TD><TD>spToProteins- Create tab delimited data files from spxxxx database for proteinsxxxx database.</TD></TR>
<TR><TD ALIGN=LEFT>spToProteinsVar:</TD><TD>spToProteinsVar- Create tab delimited data file, spXrefVar.tab,
from spYYMMDD database for proteinsYYMMDD database.</TD></TR>
<TR><TD ALIGN=LEFT>spXref3:</TD><TD>get xref data of proteins in SWISS-PROT, TrEMBL, TrEMBL-NEW and HUGO.
          Output is placed in file spXref3.tab.</TD></TR>
<TR><TD ALIGN=LEFT>spacedToTab:</TD><TD>Convert fixed width space separated fields to tab separated
Note this requires two passes, so it can't be done on a pipe</TD></TR>
<TR><TD ALIGN=LEFT>spideyToPsl:</TD><TD>Convert NCBI spidey pair alignments to PSL format</TD></TR>
 
<TR><TD ALIGN=LEFT>splitFa:</TD><TD>split a big FA file into smaller ones.</TD></TR>
<TR><TD ALIGN=LEFT>splitFaIntoContigs:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>splitFile:</TD><TD>Split up a file</TD></TR>
<TR><TD ALIGN=LEFT>splitSim:</TD><TD>Simulate gapless distribution size</TD></TR>
<TR><TD ALIGN=LEFT>spm3:</TD><TD>from all mRNAs in a genome (e.g. rn3) referenced by SWISS-PROT
      generate a list of proteins and a list of protein/mRNA pairs.</TD></TR>
<TR><TD ALIGN=LEFT>spm6:</TD><TD>generates sorted.lis and knownGene0.tab for further duplicates processing</TD></TR>
 
<TR><TD ALIGN=LEFT>spm7:</TD><TD>Create sorted list of mRNA-SP data file for further duplicates processing</TD></TR>
<TR><TD ALIGN=LEFT>sqlToXml:</TD><TD>dump out all or part of a relational database to XML, guided
by a dump specification.  See sqlToXml.doc for additional information.</TD></TR>
<TR><TD ALIGN=LEFT>stToXao:</TD><TD>make indices into st file, one for each chromosome.</TD></TR>
<TR><TD ALIGN=LEFT>stageMultiz:</TD><TD>Stage input directory for Webb's multiple aligner</TD></TR>
<TR><TD ALIGN=LEFT>stanToBedAndExpRecs:</TD><TD>takes a pslFile of alignments and a list of stanfords
expression data files and converts them into a bed file with the scores and experiment
ids. Also creates a corresponding file of expRecords which idicate what the</TD></TR>
<TR><TD ALIGN=LEFT>stitchea:</TD><TD>joins together EA files into one big one, throwing out overlaps.
Will complain if there's any missing data.</TD></TR>
 
<TR><TD ALIGN=LEFT>stitcher:</TD><TD>third pass of genomic/genomic alignment. Stitches
together 2000x5000 base 7-state alignments into longer contigs.</TD></TR>
<TR><TD ALIGN=LEFT>stringify:</TD><TD>Convert file to C strings</TD></TR>
<TR><TD ALIGN=LEFT>subChar:</TD><TD>Substitute one character for another throughout a file.</TD></TR>
<TR><TD ALIGN=LEFT>subs:</TD><TD>Subs - a utility to perform massive string substitutions on source</TD></TR>
<TR><TD ALIGN=LEFT>subsetAxt:</TD><TD>Rescore alignments and output those over threshold</TD></TR>
<TR><TD ALIGN=LEFT>subsetTraces:</TD><TD>Build subset of mouse traces that actually align</TD></TR>
 
<TR><TD ALIGN=LEFT>tableSum:</TD><TD>Summarize a table somehow</TD></TR>
<TR><TD ALIGN=LEFT>tailLines:</TD><TD>add tail to each line of file</TD></TR>
<TR><TD ALIGN=LEFT>textHist2:</TD><TD>Make two dimensional histogram table out
of a list of 2-D points, one per line.</TD></TR>
<TR><TD ALIGN=LEFT>textHistogram:</TD><TD>Make a histogram in ascii</TD></TR>
<TR><TD ALIGN=LEFT>tfbsConsLoc:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>tfbsConsSort:</TD><TD>a utility to sort tfbsCons files before loading them</TD></TR>
 
<TR><TD ALIGN=LEFT>tickToDate:</TD><TD>Convert seconds since 1970 to time and date</TD></TR>
<TR><TD ALIGN=LEFT>toDev64:</TD><TD>A program that copies data from the old hgwdev database to the
new hgwdev database.</TD></TR>
<TR><TD ALIGN=LEFT>toLower:</TD><TD>Convert upper case to lower case in file. Leave other chars alone</TD></TR>
<TR><TD ALIGN=LEFT>toUpper:</TD><TD>Convert lower case to upper case in file. Leave other chars alone</TD></TR>
<TR><TD ALIGN=LEFT>trackOverlap:</TD><TD>trackOverlap- Overlap how much of a track is overlapped by
  other tracks and vice versa. This is done by correlating
  series of bitmap projections (i.e. featureBits multiple times).</TD></TR>
<TR><TD ALIGN=LEFT>trfBig:</TD><TD>Mask tandem repeats on a big sequence file.</TD></TR>
 
<TR><TD ALIGN=LEFT>twinOrf:</TD><TD>Predict open reading frame in cDNA given a cross species alignment</TD></TR>
<TR><TD ALIGN=LEFT>twinOrf2:</TD><TD>Predict open reading frame in cDNA given a cross species alignment</TD></TR>
<TR><TD ALIGN=LEFT>twinOrf3:</TD><TD>Predict open reading frame in cDNA given a cross species alignment</TD></TR>
<TR><TD ALIGN=LEFT>twinOrfStats:</TD><TD>Collect stats on refSeq cDNAs aligned to another
species via axtForEst</TD></TR>
<TR><TD ALIGN=LEFT>twinOrfStats2:</TD><TD>Collect stats on refSeq cDNAs aligned to another
species via axtForEst</TD></TR>
<TR><TD ALIGN=LEFT>twinOrfStats3:</TD><TD>Collect stats on refSeq cDNAs aligned to another
species via axtForEst</TD></TR>
 
<TR><TD ALIGN=LEFT>twoBitInfo:</TD><TD>get information about sequences in a .2bit file</TD></TR>
<TR><TD ALIGN=LEFT>twoBitToFa:</TD><TD>Convert all or part of .2bit file to fasta</TD></TR>
<TR><TD ALIGN=LEFT>undupFa:</TD><TD>rename duplicate records in FA file
usage
  undupFa faFile(s)</TD></TR>
<TR><TD ALIGN=LEFT>updateStsInfo:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>upper:</TD><TD>strip numbers, spaces, and punctuation turn to upper case</TD></TR>
<TR><TD ALIGN=LEFT>vegaBuildInfo:</TD><TD></TD></TR>
<TR><TD ALIGN=LEFT>venn:</TD><TD>Do venn diagram calculations</TD></TR>
 
<TR><TD ALIGN=LEFT>vgPrepImage:</TD><TD>Create thumbnail and image pyramid scheme for image,
also link in full sized image</TD></TR>
<TR><TD ALIGN=LEFT>wabToSt:</TD><TD>Convert WABA output to something Intronerator understands better</TD></TR>
<TR><TD ALIGN=LEFT>whyConserved:</TD><TD>Try and analyse why a particular thing is conserved</TD></TR>
<TR><TD ALIGN=LEFT>wigEncode:</TD><TD>convert Wiggle ascii data to binary format</TD></TR>
<TR><TD ALIGN=LEFT>wordLine:</TD><TD>chop up words by white space and output them with one
word to each line.</TD></TR>
<TR><TD ALIGN=LEFT>xmlCat:</TD><TD>Concatenate xml files together, stuffing all records inside a single outer tag. </TD></TR>
 
<TR><TD ALIGN=LEFT>xmlToSql:</TD><TD>Convert XML dump into a fairly normalized relational database
  in the form of a directory full of tab-separated files and table
  creation SQL.  You'll need to run autoDtd on the XML file first to</TD></TR>
</TABLE>

Latest revision as of 19:31, 7 May 2014

The list that used to be on this page is outdated. Please see the current list here: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER

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