Kent source utilities: Difference between revisions

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More information about these tools can be found here [[Kent source utilities]].
The list that used to be on this page is outdated.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
<H3>Last updated: 2009-11-09 - 09 November 2009</H3>
<TABLE>
<TR><TD VALIGN=TOP ALIGN=LEFT>aNotB:</TD><TD>List symbols that are in a but not b</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>addAveMedScoreToPsls:</TD><TD>Combines unigene pslFile and sage file into bed file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>addCols:</TD><TD>Sum columns in a text file.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>agpAllToFaFile:</TD><TD>Convert all sequences in an .agp file to a .fa file </TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>agpCloneCheck:</TD><TD>Check that have all clones in an agp file (and the right version too)</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>agpCloneList:</TD><TD>Make simple list of all clones in agp file
to stdout</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>agpToFa:</TD><TD>Convert a .agp file to a .fa file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>agpToGl:</TD><TD>Convert AGP file to GL file.  Some fakery involved.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>agxToBed:</TD><TD>Utility program that condenses an altGraphX record
into a bed record.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>agxToTxg:</TD><TD>Convert from old altGraphX format to newer txGraph format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>ali2alx:</TD><TD>produces an index file for each chromosome into an ali file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>aliGlue:</TD><TD>tell where a cDNA is located quickly.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>allenCollectSeq:</TD><TD>Collect probe sequences for Allen Brain Atlas from a variety of sources</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>altAnalysis:</TD><TD>Analyze the altSplicing in a series of altGraphX's</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>altPaths:</TD><TD>Examin altGraphX graphs and discover alternative
splicing events and their paths.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>altSplice:</TD><TD>-help -- Display this message.
-db -- Database (i.e. hg15) to load psl records from.
-beds -- Coordinate file to base clustering on in bed format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>altSummary:</TD><TD>Summarize the altSplicing in a series of altGraphX's</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>apacheMonitor:</TD><TD>check for error 500s in the last minutes</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>assessLibs:</TD><TD>Make table that assesses the percentage of library that covers 5' and 3' ends</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>autoXml:</TD><TD>Generate structures code and parser for XML file from DTD-like spec</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>ave:</TD><TD>Compute average and basic stats</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>aveCols:</TD><TD>average together columns</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>averagExp:</TD><TD>Average expression data within a cluster</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>axtAndBed:</TD><TD>Intersect an axt with a bed file and output axt.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtBest:</TD><TD>Remove second best alignments</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtCalcMatrix:</TD><TD>Calculate substitution matrix and make indel histogram</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtChain:</TD><TD>Chain together axt alignments.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtDropOverlap:</TD><TD>deletes all overlapping self alignments. </TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>axtDropSelf:</TD><TD>Drop alignments that just align same thing to itself</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtFilter:</TD><TD>Filter axt files.  Output goes to standard out.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtForEst:</TD><TD>Generate file of mouse/human alignments corresponding to MGC EST's</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtIndex:</TD><TD>build index of axt file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtPretty:</TD><TD>Convert axt to more human readable format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtQueryCount:</TD><TD>Count bases covered on each query sequence</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>axtRecipBest:</TD><TD>create file for dot plot using recip best </TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtRescore:</TD><TD>Recalculate scores in axt.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtSort:</TD><TD>Sort axt files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtSplitByTarget:</TD><TD>Split a single axt file into one file per target</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtSwap:</TD><TD>Swap source and query in an axt file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtToBed:</TD><TD>Convert axt alignments to simple bed format</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>axtToChain:</TD><TD>Convert axt to chain format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtToMaf:</TD><TD>Convert from axt to maf format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>axtToPsl:</TD><TD>Convert axt to psl format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedClip:</TD><TD>Remove lines from bed file that refer to off-chromosome places.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedCons:</TD><TD>Look at conservation of a BED track vs. a refence (nonredundant) alignment track</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedCoverage:</TD><TD>Analyse coverage by bed files - chromosome by
chromosome and genome-wide.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>bedDown:</TD><TD>Make stuff to find a BED format submission in a new version</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedExtendRanges:</TD><TD>extend length of entries in bed 6+ data to be at least the given length,
taking strand directionality into account.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedGraphToBigWig:</TD><TD>Convert a bedGraph program to bigWig.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedInGraph:</TD><TD>Program to determine if bed exons are contained in
a splice graph. Original motivation to see which alt-spliced
probe sets are also alt in human (in addition to mouse).</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedIntersect:</TD><TD>Intersect two bed files</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>bedOrBlocks:</TD><TD>Create a bed that is the union of all blocks of a list of beds.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedSort:</TD><TD>Sort a .bed file by chrom,chromStart</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedSplitOnChrom:</TD><TD>Split bed into a directory with one file per chromosome.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedToBigBed:</TD><TD>Convert bed file to bigBed.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedToExons:</TD><TD>Split a bed up into individual beds.
One for each internal exon.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedToFrames:</TD><TD>Makes html files for browsing custom bed track
using frames. Use -pad for padding</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>bedToGenePred:</TD><TD>Too few arguments:
convert bed format files to genePred format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedToTxEdges:</TD><TD>Convert a bed file into txEdgeBed, which can be used with txgAddEvidence.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedUp:</TD><TD>Load bed submissions after conversion back into new database.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bedWeedOverlapping:</TD><TD>Filter out beds that overlap a 'weed.bed' file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bigBedSummary:</TD><TD>Extract summary information from a bigBed file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bigBedToBed:</TD><TD>Convert from bigBed to ascii bed format.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>bigWigInfo:</TD><TD>Print out information about bigWig file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bigWigSummary:</TD><TD>Extract summary information from a bigWig file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bigWigToBedGraph:</TD><TD>Convert from bigWig to bedGraph format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>binGood:</TD><TD>convert text format alignment file to binary format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>blastRecipBest:</TD><TD>Pick out just the reciprocal best alignments.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>blastToPsl:</TD><TD>Convert blast alignments to PSLs.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>blat:</TD><TD>Standalone BLAT v. 34x5 fast sequence search command line tool</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>blatz:</TD><TD>blatz version 1 - Align dna across species</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>blatzClient:</TD><TD>blatzClient version 1 - Ask server to do
cross-species DNA alignments and save results.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>blatzServer:</TD><TD>blatzServer version 1 - Set up in-memory server for
cross-species DNA alignments</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>borfBig:</TD><TD>Run Victor Solovyev's bestorf repeatedly</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bottleneck:</TD><TD>bottleneck v2 - A server that helps slow down hyperactive web robots</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>bptForTwoBit:</TD><TD>Create a b+ tree index for a .2bit file.  Key is the sequence name. Value
is the position of the start of the compressed DNA in the .2bit file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bptLookupStringToBits64:</TD><TD>Given a string value look up and return associated 64 bit value if
any.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bptMakeStringToBits64:</TD><TD>Create a B+ tree index with string keys and unsigned 64-bit-integer
values. In practice the 64-bit values are often offsets in a file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>bwana:</TD><TD>do batch coarse alignment of C. briggsae and C. elegans genomes.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>calc:</TD><TD>Little command line calculator</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>calcGap:</TD><TD>calculate gap scores</TD></TR>
 
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>catUncomment:</TD><TD>Concatenate input removing lines that start with '#'
Output goes to stdout</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>cdnaOff:</TD><TD>creates sorted offset files that position cDNAs in chromosome.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chainAntiRepeat:</TD><TD>Get rid of chains that are primarily the results of repeats and degenerate DNA</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chainDbToFile:</TD><TD>translate a chain's db representation back to file</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>chainFilter:</TD><TD>Filter chain files.  Output goes to standard out.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chainMergeSort:</TD><TD>Combine sorted files into larger sorted file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chainNet:</TD><TD>Make alignment nets out of chains</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chainPreNet:</TD><TD>Remove chains that don't have a chance of being netted</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>chainSplit:</TD><TD>Split chains up by target or query sequence</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>chainStats:</TD><TD>Stitch psls into chains</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chainStitchId:</TD><TD>Join chain fragments with the same chain ID into a single
chain per ID.  Chain fragments must be from same original chain but
must not overlap.  Chain fragment scores are summed.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chainSwap:</TD><TD>Swap target and query in chain</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chainToAxt:</TD><TD>Convert from chain to axt file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chainToPsl:</TD><TD>Convert chain file to psl format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>checkAgpAndFa:</TD><TD>takes a .agp file and .fa file and ensures that they are in synch</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>checkCardinality:</TD><TD>reviewIndexes - check indexes</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>checkChain:</TD><TD>read all chains and report if duplicate ids</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>checkHgFindSpec:</TD><TD>test and describe search specs in hgFindSpec tables.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>checkSgdSync:</TD><TD>Make sure that genes and sequence are in sync for
SGD yeast database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>checkTableCoords:</TD><TD>check invariants on genomic coords in table(s).</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>checkableBorf:</TD><TD>Convert borfBig orf-finder output to checkable form</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>chopFaLines:</TD><TD>Read in FA file with long lines and rewrite it with shorter lines</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chromGraphFromBin:</TD><TD>Convert chromGraph binary to ascii format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>chromGraphToBin:</TD><TD>Make binary version of chromGraph.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>clusterGenes:</TD><TD>Cluster genes from genePred tracks</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>clusterPsl:</TD><TD>Make clusters of mRNA aligments</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>clusterRna:</TD><TD>Make clusters of mRNA and ESTs</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>consForBed:</TD><TD>Takes a bed file and a conservation file and outputs
conservation scores for each position in the bed file. Optionally
outputs a summary file which contains every conservation value seen</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>convolve:</TD><TD>perform convolution of probabilities</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>countChars:</TD><TD>Count the number of occurences of a particular char</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>crTreeIndexBed:</TD><TD>Create an index for a bed file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>crTreeSearchBed:</TD><TD>Search a crTree indexed bed file and print all items that overlap query.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>ctgFaToFa:</TD><TD>Convert from one big file with all NT contigs to one contig per file.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>ctgToChromFa:</TD><TD>convert contig level fa files to chromosome level</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>dbFindFieldsWith:</TD><TD>Look through database and find fields that have elements matching a certain regular expression in the first N rows.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>dbSnoop:</TD><TD>Produce an overview of a database.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>dbTrash:</TD><TD>drop tables from a database older than specified N hours</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>detab:</TD><TD>remove tabs from program</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>dnaMotifFind:</TD><TD>Locate preexisting motifs in DNA sequence</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>eisenInput:</TD><TD>Create input for Eisen-style cluster program</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>emblMatrixToMotif:</TD><TD>Convert transfac matrix in EMBL format to dnaMotif</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>embossToPsl:</TD><TD>Convert EMBOSS pair alignments to PSL format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>endsInLf:</TD><TD>Check that last letter in files is end of line</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>estLibStats:</TD><TD>Calculate some stats on EST libraries given file from polyInfo</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>estOrient:</TD><TD>estOrient [options] db estTable outPsl</TD></TR>
 
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>expToRna:</TD><TD>Make a little two column table that associates
rnaClusters with expression info</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faAlign:</TD><TD>Align two fasta files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faCmp:</TD><TD>Compare two .fa files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faCount:</TD><TD>count base statistics and CpGs in FA files.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faFilter:</TD><TD>Filter fa records, selecting ones that match the specified conditions</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>faFilterN:</TD><TD>Get rid of sequences with too many N's</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faFlyBaseToUcsc:</TD><TD>Convert Flybase peptide fasta file to UCSC format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faFrag:</TD><TD>Extract a piece of DNA from a .fa file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faGapLocs:</TD><TD>report location of gaps and sequences in a FASTA file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faGapSizes:</TD><TD>report on gap size counts/statistics</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faNcbiToUcsc:</TD><TD>Convert FA file from NCBI to UCSC format.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>faNoise:</TD><TD>Add noise to .fa file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faOneRecord:</TD><TD>Extract a single record from a .FA file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faPolyASizes:</TD><TD>get poly A sizes</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faRandomize:</TD><TD>Program to create random fasta records using
same base frequency as seen in original fasta records.
Use optional -seed flag to specify seed for random number</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faRc:</TD><TD>Reverse complement a FA file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faSimplify:</TD><TD>Simplify fasta record headers</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>faSize:</TD><TD>print total base count in fa files.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faSomeRecords:</TD><TD>Extract multiple fa records</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faSplit:</TD><TD>Split an fa file into several files.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faToFastq:</TD><TD>Convert fa to fastq format, just faking quality values.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faToNib:</TD><TD>Convert from .fa to .nib format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faToTab:</TD><TD>convert fa file to tab separated file</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>faToTwoBit:</TD><TD>Convert DNA from fasta to 2bit format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faTrans:</TD><TD>Translate DNA .fa file to peptide</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faTrimPolyA:</TD><TD>trim poly-A tails</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>faTrimRead:</TD><TD>trim reads based on qual scores - change low scoring bases to N's </TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>fakeFinContigs:</TD><TD>Fake up contigs for a finished chromosome</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>fakeOut:</TD><TD>fake a RepeatMasker .out file based on a N's in .fa file</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>fastqToFa:</TD><TD>Convert from fastq to fasta format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>fatont4:</TD><TD>fato4nt - a program to convert .fa files to .4nt files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>featureBits:</TD><TD>Correlate tables via bitmap projections. </TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>ffaToFa:</TD><TD>ffaToFa convert Greg Schuler .ffa fasta files to UCSC .fa fasta files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>findMotif:</TD><TD>find specified motif in sequence</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>fixCr:</TD><TD>strip <CR>s from ends of lines</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>fixHarbisonMotifs:</TD><TD>Trim motifs that have beginning or ending columns that are degenerate.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>fqToQa:</TD><TD>convert from fq format with one big file to
format with one file per clone.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>fragPart:</TD><TD>get part of a fragment's sequence</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gadPos:</TD><TD> generate genomic positions for GAD entries</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>gapSplit:</TD><TD>split sequence on gaps of size >= N</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gapToLift:</TD><TD>create lift file from gap table(s)</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gb2cdi:</TD><TD>convert GeneBank (GB) files to .fa and cDna Info (CDI) file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gbGetEntries:</TD><TD>retrieve records from a GenBank flat file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gbOneAcc:</TD><TD>retrieve one or a few records from a GenBank flat file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gbSeqCheck:</TD><TD>check that extFile references in gbSeq table are valid</TD></TR>
 
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>gbtofa:</TD><TD>gbtofa converts from GeneBank to fa format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gcForBed:</TD><TD>Calculate g/c percentage and other stats for regions covered by bed</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>genePredCheck:</TD><TD>validate genePred files or tables</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>genePredHisto:</TD><TD>wrong number of arguments
get data for generating histograms from a genePred file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>genePredSingleCover:</TD><TD>wrong # args
create single-coverage genePred files</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>genePredToFakePsl:</TD><TD>Create a psl of fake-mRNA aligned to gene-preds from a file or table.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>genePredToGtf:</TD><TD>Convert genePred table or file to gtf.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>genePredToMafFrames:</TD><TD>wrong # args
create mafFrames tables from a genePreds</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>genePredToPsl:</TD><TD>Program to create fake psl alignments from
genePred records. Originally designed for use with altSplice.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>geniegff:</TD><TD>makes up a gdf file from Genie gene predictions</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>getChroms:</TD><TD>print chrom names</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>getFeatDna:</TD><TD>Get dna for a type of feature</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>getRna:</TD><TD>Get mrna for GenBank or RefSeq sequences found in a database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>getRnaPred:</TD><TD>Get virtual RNA for gene predictions</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gfClient:</TD><TD>gfClient v. 34x5 - A client for the genomic finding program that produces a .psl file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gfPcr:</TD><TD>In silico PCR version 34x5 using gfServer index.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gfServer:</TD><TD>gfServer v 34x5 - 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 VALIGN=TOP ALIGN=LEFT>gff3ToGenePred:</TD><TD>convert a GFF3 file to a genePred file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gffPeek:</TD><TD>Look at a gff file and report some basic stats</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gffgenes:</TD><TD>creates files that store extents of genes for intronerator</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gmtime:</TD><TD>convert unix timestamp to date string</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gpStats:</TD><TD>Figure out some stats on the golden path.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gpToGtf:</TD><TD>Convert gp table to GTF</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>gpcrParser:</TD><TD>Create xml files for gpcr snakeplots.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>gsBig:</TD><TD>Run Genscan on big input and produce GTF files and other parsed output</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>gtfToGenePred:</TD><TD>convert a GTF file to a genePred</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hapmapPhaseIIISummary:</TD><TD>Make hapmapPhaseIIISummary.bed from hapmap*.bed.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>headRest:</TD><TD>Return all *but* the first N lines of a file.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgAddLiftOverChain:</TD><TD>Add a liftOver chain to the central database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgAvidShortBed:</TD><TD>Convert short form of AVID alignments to BED</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgBbiDbLink:</TD><TD>Add table that just contains a pointer to a bbiFile to database.  This program
is used to add bigWigs and bigBeds.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgBioCyc:</TD><TD>bioCyc - Creates bioCycPathway.tab for Known Genes to link to SRI BioCyc pathways</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgCeOrfToGene:</TD><TD>Make orfToGene table for C.elegans from GENE_DUMPS/gene_names.txt</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgChroms:</TD><TD>print chromosomes for a genome.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgClonePos:</TD><TD>create clonePos table in browser database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgClusterGenes:</TD><TD>Cluster overlapping gene predictions</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgCountAlign:</TD><TD>count overlaping or non-overlaping windows in an alignment.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgCtgPos:</TD><TD>Store contig positions ( from lift files ) in database.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgDeleteChrom:</TD><TD>output SQL commands to delete a chrom from the database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgDropSplitTable:</TD><TD>Drop a table, or drop all tables in a split table</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgEmblProtLinks:</TD><TD>Parse EMBL flat file into protein link table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgExonerate:</TD><TD>Convert Exonerate modified GFF files to BED format and load in database.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgExpDistance:</TD><TD>Create table that measures expression distance between pairs</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgExperiment:</TD><TD>Load data from a BED of region positions,
an experiment file containing <name> [<description>]</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgExtFileCheck:</TD><TD>check extFile or gbExtFile tables against file system</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgFakeAgp:</TD><TD>Create fake AGP file by looking at N's</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgFiberglass:</TD><TD>Turn Fiberglass Annotations into a BED and load into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgFindSpec:</TD><TD>Create hgFindSpec table from trackDb.ra files.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgFlyBase:</TD><TD>Parse FlyBase genes.txt file and turn it into a couple of tables</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgGcPercent:</TD><TD>Calculate GC Percentage in 20kb windows</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgGeneBands:</TD><TD>Find bands for all genes</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgGenericMicroarray:</TD><TD>Load generic microarray file into database.
A generic microarray file has the following format: </TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgGetAnn:</TD><TD>get chromosome annotation rows from database tables using
browser-style position specification.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgGnfMicroarray:</TD><TD>Load data from (2003-style) GNF Affy Microarrays</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgGoAssociation:</TD><TD>Load bits we care about in GO association table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgGoldGapGl:</TD><TD>Put chromosome .agp and .gl files into browser database.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgJaxQtl:</TD><TD>generate bed file for jaxQTL3 table
using the table jaxQtlRaw as input
output file is jaxQTL3.tab.</TD></TR>
 
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>hgKegg3:</TD><TD>creates keggPathway.tab and keggMapDesc.tab files for KG links to KEGG Pathway Mapusage:
hgKegg3 kgTempDb roDb
kgTempDb is the KG build temp database name</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>hgKnownGeneList:</TD><TD>Generate Known Genes List HTML pages to be indexed by Google</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgKnownMore:</TD><TD>Create the knownMore table from a variety of sources.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgKnownToSuper:</TD><TD>Load knownToSuperfamily table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadBed:</TD><TD>Load a generic bed file into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadBlastTab:</TD><TD>Load blast table into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadChain:</TD><TD>Load a generic Chain file into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadChromGraph:</TD><TD>Load up chromosome graph.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadEranModules:</TD><TD>Load regulatory modules from Eran Segal</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadGap:</TD><TD>Load gap table from AGP-style file containing only gaps</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadGenePred:</TD><TD>wrong # args
Load up a mySQL database genePred table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadItemAttr:</TD><TD>load an itemAttr table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadMaf:</TD><TD>Load a maf file index into the database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadMafFrames:</TD><TD>wrong # args
load an mafFrames table</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadNet:</TD><TD>Load a generic net file into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadNetDist:</TD><TD>GS loader for interaction network path lengths.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadOut:</TD><TD>load RepeatMasker .out files into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadPsl:</TD><TD>Load up a mySQL database with psl alignment tables</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadRnaFold:</TD><TD>Load a directory full of RNA fold files into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadSample:</TD><TD>Load a sample 9 (wiggle) file into database</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadSeq:</TD><TD>load browser database with sequence file info.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadSqlTab:</TD><TD>Load table into database from SQL and text files.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLoadWiggle:</TD><TD>Load a wiggle track definition into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgLsSnpPdbLoad:</TD><TD>fetch data from LS-SNP/PDB mysql server or
load an lsSnpPdb format table or file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgMapMicroarray:</TD><TD>Make mapped version of microarray data, merging psl in.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgMapToGene:</TD><TD>Map a track to a genePred track.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgMapViaSwissProt:</TD><TD>Make table that maps to external database via SwissProt</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgMedianMicroarray:</TD><TD>Create a copy of microarray database that contains the
median value of replicas</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>hgNearTest:</TD><TD>Test hgNear web page</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgNetDist:</TD><TD>GS loader for gene/protein interaction network distances.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgNibSeq:</TD><TD>convert DNA to nibble-a-base and store location in database</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgPepPred:</TD><TD>Load peptide predictions from Ensembl or Genie</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgPhMouse:</TD><TD>Load phMouse track</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgProtIdToGenePred:</TD><TD>Add proteinID column to genePrediction</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgRatioMicroarray:</TD><TD>Create a ratio form of microarray data.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgRenameSplitTable:</TD><TD>Rename a table, or rename all tables in a split table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgRnaGenes:</TD><TD>Turn RNA genes from GFF into database format (BED variant)</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSanger20:</TD><TD>Load extra info from Sanger Chromosome 20 annotations.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSanger22:</TD><TD>Load up database with Sanger 22 annotations</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSelect:</TD><TD>select from genome tables, handling split tables and
bin column</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSgdGff3:</TD><TD>Parse out SGD gff3 file into components</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSgdGfp:</TD><TD>Parse localization files from SGD and Load Database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSgdPep:</TD><TD>Parse yeast protein fasta files into format we can load</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSoftPromoter:</TD><TD>Slap Softberry promoter file into database.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSoftberryHom:</TD><TD>Make table storing Softberry protein homology information</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSpeciesRna:</TD><TD>Create fasta file with RNA from one species</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgStanfordMicroarray:</TD><TD>Load up from Stanford Microarray Database files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgStsAlias:</TD><TD>Make table of STS aliases</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgStsMarkers:</TD><TD>Load STS markers into database</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgSuperfam:</TD><TD>Generate supfamily table for the Superfamily track.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgTablesTest:</TD><TD>Test hgTables web page</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgTpf:</TD><TD>Make TPF table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgTraceInfo:</TD><TD>import subset of mouse trace ancillary information
parsed from FASTA files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgTrackDb:</TD><TD>Create trackDb table from text files.
Note that the browser supports multiple trackDb tables, usually</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgTracksRandom:</TD><TD>November 09, 2009 11:50
Time default view for random position of default genome</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgWaba:</TD><TD>load Waba alignments into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT> [[Using_hgWiggle_without_a_database | hgWiggle]]:</TD><TD>fetch wiggle data from data base or file</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>hgYeastRegCode:</TD><TD>Load files from the regulatory code paper (large scale
CHIP-CHIP on yeast) into database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgsql:</TD><TD>Execute some sql code using passwords in .hg.conf</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgsqlLocal:</TD><TD>Execute some sql code using localDb.XXX in .hg.conf</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>hgsqladmin:</TD><TD>Wrapper around mysqladmin using passwords in .hg.conf</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgsqldump:</TD><TD>Execute mysqldump using passwords from .hg.conf</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgsqldumpLocal:</TD><TD>Execute mysqldump using passwords from .hg.conf</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hgsqlimport:</TD><TD>Execute mysqlimport using passwords from .hg.conf</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hmmPfamToTab:</TD><TD>Convert hmmPfam output to something simple and tab-delimited.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>hprdP2p:</TD><TD>Create hprd.p2p tab file using HPRD flat file for input to hgNetDist</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>htmlCheck:</TD><TD>Do a little reading and verification of html file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>htmlPics:</TD><TD>create an html file from a list of pictures
usage
htmlPics picFile(s)</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>indexfa:</TD><TD>This program makes an index file for a .fa file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>indexgl:</TD><TD>This program makes an index file for a .gl file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>intronEnds:</TD><TD>Gather stats on intron ends.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>introns:</TD><TD>Introns - finds the introns in a file and writes them to gff.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>iriToControlTable:</TD><TD>Convert improbizer run to simple list of control scores</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>iriToDnaMotif:</TD><TD>Convert improbRunInfo to dnaMotif</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>isPcr:</TD><TD>Standalone v 34x5 In-Situ PCR Program</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>ixIxx:</TD><TD>Create indices for simple line-oriented file of format
<symbol> <free text></TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>ixali:</TD><TD>This program makes a name index file for an .ali file</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>joinableFields:</TD><TD>Return list of good join targets for a table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>joinerCheck:</TD><TD>Parse and check joiner file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>kgAliasKgXref:</TD><TD>create gene alias .tab file usage:
kgAliasKgXref xxxx
xxxx is genome database name</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>kgAliasRefseq:</TD><TD>create gene alias .tab file usage:
kgAliasRefseq xxxx
xxxx is genome database name</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>kgCheck:</TD><TD>from gene candidates, go through various criteria and keep the ones that pass the criteria </TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>kgGetCds:</TD><TD>create a gene candidate table with CDS info</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>kgGetPep:</TD><TD>generate FASTA format protein sequence file to be used for Known Genes track build.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>kgPick:</TD><TD>select the best repersentative mRNA/protein pair</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>kgProtAlias:</TD><TD>create protein alias .tab files usage:
kgProtAlias xxxx yyyy
xxxx is genome  database name</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>kgPutBack:</TD><TD>from gene candidates, go through various criteria and keep the ones that pass the criteria </TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>knownToHprd:</TD><TD>Create knownToHprd table using HPRD flat file and kgXref</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>knownToVisiGene:</TD><TD>Create knownToVisiGene table by riffling through various other knownTo tables</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>knownVsBlat:</TD><TD>Categorize BLAT mouse hits to known genes</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>kvsSummary:</TD><TD>Summarize output of a bunch of knownVsBlats</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>lavToAxt:</TD><TD>Convert blastz lav file to an axt file (which includes sequence)</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>lavToPsl:</TD><TD>Convert blastz lav to psl format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>ldHgGene:</TD><TD>load database with gene predictions from a gff file.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>libScan:</TD><TD>Scan libraries to help find g' capped ones</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>liftAcross:</TD><TD>convert one coordinate system to another, no overlapping items</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>liftFrags:</TD><TD>This program lifts annotations on clone fragments
to FPC contig coordinates</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>liftOver:</TD><TD>Move annotations from one assembly to another</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>liftOverMerge:</TD><TD>Merge multiple regions in BED 5 files
generated by liftOver -multiple</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>liftPromoHits:</TD><TD>Lift motif hits from promoter to chromosome coordinates</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>liftUp:</TD><TD>change coordinates of .psl, .agp, .gap, .gl, .out, .gff, .gtf .bscore
.tab .gdup .axt .chain .net, genePred, .wab, .bed, or .bed8 files to parent
coordinate system.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>lineCount:</TD><TD>Count lines in a file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>linesToRa:</TD><TD>generate .ra format from lines with pipe-separated fields</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>localtime:</TD><TD>convert unix timestamp to date string</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafAddIRows:</TD><TD>add 'i' rows to a maf</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>mafAddQRows:</TD><TD>Add quality data to a maf</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafCoverage:</TD><TD>Analyse coverage by maf files - chromosome by
chromosome and genome-wide.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafFetch:</TD><TD>get overlapping records from an MAF using an index table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafFilter:</TD><TD>Filter out maf files. Output goes to standard out</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafFrag:</TD><TD>Extract maf sequences for a region from database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafFrags:</TD><TD>Collect MAFs from regions specified in a 6 column bed file</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>mafGene:</TD><TD>output protein alignments using maf and genePred</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafMeFirst:</TD><TD>Move component to top if it is one of the named ones. 
Useful in conjunction with mafFrags when you don't want the one with
the gene name to be in the middle.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafOrder:</TD><TD>order components within a maf file</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>mafSpeciesList:</TD><TD>Scan maf and output all species used in it.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafSpeciesSubset:</TD><TD>Extract a maf that just has a subset of species.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>mafSplit:</TD><TD>Split multiple alignment files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafSplitPos:</TD><TD>Pick positions to split multiple alignment input files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafToAxt:</TD><TD>Convert from maf to axt format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafToPsl:</TD><TD>Convert maf to psl format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mafsInRegion:</TD><TD>Extract MAFS in a genomic region</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>makeTableDescriptions:</TD><TD>Add table descriptions to database.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>makepgo:</TD><TD>Make Predicted Gene Offset files.  One for each chromosome.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>mdToNcbiLift:</TD><TD>Convert seq_contig.md file to ncbi.lft</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mgcFastaForBed:</TD><TD>Take a bed file and return a fasta file
with exons uppercase and introns lowercase.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mktime:</TD><TD>convert date string to unix timestamp</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>moresyn:</TD><TD>find more gene/ORF synonyms</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>motifLogo:</TD><TD>Make a sequence logo out of a motif.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>motifSig:</TD><TD>Combine info from multiple control runs and main improbizer run</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mousePoster:</TD><TD>Search database info for making foldout</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>mrnaToGene:</TD><TD>convert PSL alignments of mRNAs to gene annotations</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>netChainSubset:</TD><TD>Create chain file with subset of chains that appear in the net</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>netClass:</TD><TD>Add classification info to net</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>netSplit:</TD><TD>Split a genome net file into chromosome net files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>netStats:</TD><TD>Gather statistics on net</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>netSyntenic:</TD><TD>Add synteny info to net.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>netToAxt:</TD><TD>Convert net (and chain) to axt.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>netToBed:</TD><TD>Convert target coverage of net to a bed file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>netToBedWithId:</TD><TD>Convert net (and chain) to bed with base identity in score.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>newProg:</TD><TD>make a new C source skeleton.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>nibFrag:</TD><TD>Extract part of a nib file as .fa (all bases/gaps lower case by default)</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>nibSize:</TD><TD>print size of nibs</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>nibbImageProbes:</TD><TD>Collect image probes for NIBB Xenopus Laevis in-situs</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>nibbNameFix:</TD><TD>Regularize format of NIBB sequence names</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>nibbParseImageDir:</TD><TD>Look through nibb image directory and allowing for typos and the like create a table that maps a file name to clone name, developmental stage, and view of body part</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>nibbPrepImages:</TD><TD>Set up NIBB frog images for VisiGene virtual
microscope - copying them to a directory and makeing up pyramid scheme.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>nt4Frag:</TD><TD>Extract a piece of a .nt4 file to .fa format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>oligoMatch:</TD><TD>find perfect matches in sequence.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>orf:</TD><TD>Find orf for cDNAs</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>orfStats:</TD><TD>Collect stats on orfs</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>orthoEvaluate:</TD><TD>Evaluate the coding potential of a bed.
(version: .c,v 1.13 2008/09/03 19:20:51 markd )
-help -- Display this message.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>orthoPickIntron:</TD><TD>Pick best intron from orthoEval.
(version: 1.8 2008/09/03 19:20:52 markd )
-help -- Display this message.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>orthoSplice:</TD><TD>program to compare splicing in different organisms
initially human and mouse as they both have nice EST and cDNA data
still working out algorithm but options are:</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>orthologBySynteny:</TD><TD>Find syntenic location for a list of gene predictions on a single chromosome</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>overlapSelect:</TD><TD>wrong # args:  overlapSelect [options] selectFile inFile outFile
Select records based on overlapping chromosome ranges.  The ranges are</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>pbCalDist:</TD><TD>pbCalDist- Create tab delimited data files to be used by Proteome Browser stamps.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pbCalDistGlobal:</TD><TD>pbCalDistGlobal- Create tab delimited data files to be used by Proteome Browser stamps.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pbCalPi:</TD><TD>Calculate pI values from a list of protein IDs </TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>pbCalResStd:</TD><TD>pbCalResStd calculates the avg frequency and standard deviation of every AA residues of the proteins in a specific genome</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pbCalResStdGlobal:</TD><TD>pbCalResStd calculates the avg frequency and standard deviation of every AA residues of the proteins in a protein database</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pbHgnc:</TD><TD>process HGNC data</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pepPredToFa:</TD><TD>Convert a pepPred table to fasta format</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>phToPsl:</TD><TD>Convert from Pattern Hunter to PSL format</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>polyInfo:</TD><TD>Collect info on polyAdenylation signals etc</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>positionalTblCheck:</TD><TD>check that positional tables are sorted</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>promoSeqFromCluster:</TD><TD>Get promoter regions from cluster</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslCDnaFilter:</TD><TD>Filter cDNA alignments in psl format. Filtering criteria are</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslCat:</TD><TD>concatenate psl files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslCheck:</TD><TD>validate PSL files</TD></TR>
 
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>pslDiff:</TD><TD>Compare queries in two or more psl files </TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslDropOverlap:</TD><TD>deletes all overlapping self alignments. </TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslFilter:</TD><TD>filter out psl file
pslFilter in.psl out.psl </TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>pslHisto:</TD><TD>pslHisto [options] what inPsl outHisto</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>pslHitPercent:</TD><TD>Figure out percentage of reads in FA file that hit.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslIntronsOnly:</TD><TD>Filter psl files to only include those with introns</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>pslMrnaCover:</TD><TD>Make histogram of coverage percentage of mRNA in psl.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslPartition:</TD><TD>split PSL files into non-overlapping sets</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslPretty:</TD><TD>Convert PSL to human readable output</TD></TR>
 
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>pslReps:</TD><TD>analyse repeats and generate genome wide best
alignments from a sorted set of local alignments</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslSelect:</TD><TD>select records from a PSL file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslSimp:</TD><TD>create simplified version of psl file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslSort:</TD><TD>merge and sort psCluster .psl output files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslSortAcc:</TD><TD>sort pslSort .psl output file by accession
Make one output .psl file per accession.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>pslSplitOnTarget:</TD><TD>Split psl files into one per target.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslStats:</TD><TD>collect statistics from a psl file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslSwap:</TD><TD>wrong # args:
pslSwap [options] inPsl outPsl</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslToBed:</TD><TD>pslToBed: tranform a psl format file to a bed format file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslToPslx:</TD><TD>Convert from psl to pslx format, which includes sequences</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslToXa:</TD><TD>Convert from psl to xa alignment format</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>pslUnpile:</TD><TD>Removes huge piles of alignments from sorted
psl files (due to unmasked repeats presumably).</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>pslxToFa:</TD><TD>convert pslx (with sequence) to fasta file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>qaToQac:</TD><TD>convert from uncompressed to compressed
quality score format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>qacAgpLift:</TD><TD>Use AGP to combine per-scaffold qac into per-chrom qac.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>qacToQa:</TD><TD>convert from compressed to uncompressed
quality score format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>qacToWig:</TD><TD>convert from compressed quality score format to wiggle format.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>raToCds:</TD><TD>Extract CDS positions from ra file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>raToLines:</TD><TD>Output .ra file stanzas as single lines, with pipe-separated fields.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>raToTab:</TD><TD>Convert ra file to table.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>randomLines:</TD><TD>Pick out random lines from file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>refiAli:</TD><TD>This program turns rough alignments into fine ones.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>refreshNamedSessionCustomTracks:</TD><TD>refreshNamedSessionCustomTracks -- scan central database's namedSessionDb
contents for custom tracks and touch any that are found, to prevent
them from being removed by the custom track cleanup process.</TD></TR>
 
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>relPairs:</TD><TD>extract pairs from a big pair list file that actually
occur in a .psl file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>reviewIndexes:</TD><TD>check indexes</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>reviewSanity:</TD><TD>Look through sanity files and make sure things are ok.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>rikenBestInCluster:</TD><TD>Find best looking in Riken cluster</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>rmFaDups:</TD><TD>rmFaDup - remove duplicate records in FA file
usage
rmFaDup oldName.fa newName.fa</TD></TR>
 
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>rnaFoldBig:</TD><TD>Run RNAfold repeatedly</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>rowsToCols:</TD><TD>Convert rows to columns and vice versa in a text file.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>samHit:</TD><TD>reads the SAM output .rdb file and produce .tab data for the protHomolog table. usage:
samHit proteinId rdbFN
proteinId is the protein ID</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>sanger22gtf:</TD><TD>Convert Sanger chromosome 22 annotations to gtf</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>scaffoldFaToAgp:</TD><TD>generate an AGP file, gap file, and lift file from a scaffold FA file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>scaleSampleFiles:</TD><TD>scale all of the scores in a file by a scale factor.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>scanRa:</TD><TD>scan through ra files for info.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>scopCollapse:</TD><TD>Convert SCOP model to SCOP ID. Also make id/name converter file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>scrambleFa:</TD><TD>scramble the order of records in an fa file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>seqCheck:</TD><TD>check that extFile references in seq table are valid</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>sequenceForBed:</TD><TD>Writes sequence for beds to a fasta
file. Requires database access.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>sim4big:</TD><TD>A wrapper for Sim4 that runs it repeatedly on a multi-sequence .fa file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>simpleChain:</TD><TD>Stitch psls into chains</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>sizeof:</TD><TD>type  bytes    bits
char 1 8
unsigned char 1 8</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>snpException:</TD><TD>Get exceptions to a snp invariant rule.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>snpMaskAddInsertions:</TD><TD>snpMaskAddInsertions -- Print genomic sequence plus insertion SNPs.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>snpMaskCutDeletions:</TD><TD>snpMaskCutDeletions -- Print genomic sequence with deletion SNPs removed.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>snpMaskSingle:</TD><TD>print sequence using IUPAC ambiguous nucleotide codes for single base substitutions</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>snpNcbiToUcsc:</TD><TD>Reformat NCBI SNP field values into UCSC, and flag exceptions.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>snpValid:</TD><TD>Validate snp alignments</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>sortFilt:</TD><TD>merge, sort, and filter patSpace .hit output.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>spLoadRankProp:</TD><TD>load swissprot rankProp table.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>spTest:</TD><TD>Test out sp library.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>spToDb:</TD><TD>Create a relational database out of SwissProt/trEMBL flat files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>spToProteins:</TD><TD>spToProteins- Create tab delimited data files from spxxxx database for proteinsxxxx database.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>spToProteinsVar:</TD><TD>spToProteinsVar- Create tab delimited data file, spXrefVar.tab,
from spYYMMDD database for proteinsYYMMDD database.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>spToSpXref2:</TD><TD>spToSpXref2- Create tab delimited data files for the spXref2 table in uniProt (spxxxxxx) database.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>spideyToPsl:</TD><TD>Convert NCBI spidey pair alignments to PSL format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>splitFa:</TD><TD>split a big FA file into smaller ones.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>splitFile:</TD><TD>Split up a file</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>splitFileByColumn:</TD><TD>Split text input into files named by column value</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>splitSim:</TD><TD>Simulate gapless distribution size</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>spm6:</TD><TD>generates sorted.lis and knownGene0.tab for further duplicates processing</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>spm7:</TD><TD>Create sorted list of mRNA-SP data file for further duplicates processing</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>stToXao:</TD><TD>make indices into st file, one for each chromosome.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>stageMultiz:</TD><TD>Stage input directory for Webb's multiple aligner</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>stringify:</TD><TD>Convert file to C strings</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>subChar:</TD><TD>Substitute one character for another throughout a file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>subColumn:</TD><TD>Substitute one column in a tab-separated file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>subs:</TD><TD>Subs - a utility to perform massive string substitutions on source</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>subsetAxt:</TD><TD>Rescore alignments and output those over threshold</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>subsetTraces:</TD><TD>Build subset of mouse traces that actually align</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>tableSum:</TD><TD>Summarize a table somehow</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>tailLines:</TD><TD>add tail to each line of file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>testSearch:</TD><TD>test search functionality.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>textHistogram:</TD><TD>Make a histogram in ascii</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>tfbsConsSort:</TD><TD>a utility to sort tfbsCons files before loading them</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>tickToDate:</TD><TD>Convert seconds since 1970 to time and date</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>timePosTable:</TD><TD>time access to a positional table</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>toDev64:</TD><TD>A program that copies data from the old hgwdev database to the
new hgwdev database.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>toLower:</TD><TD>Convert upper case to lower case in file. Leave other chars alone</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>toUpper:</TD><TD>Convert lower case to upper case in file. Leave other chars alone</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>trackDbRaFormat:</TD><TD>Format trackDb.ra canonically.</TD></TR>
<TR><TD VALIGN=TOP 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 VALIGN=TOP ALIGN=LEFT>trfBig:</TD><TD>Mask tandem repeats on a big sequence file.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>twinOrf:</TD><TD>Predict open reading frame in cDNA given a cross species alignment</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>twinOrf2:</TD><TD>Predict open reading frame in cDNA given a cross species alignment</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>twinOrf3:</TD><TD>Predict open reading frame in cDNA given a cross species alignment</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>twinOrfStats:</TD><TD>Collect stats on refSeq cDNAs aligned to another
species via axtForEst</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>twinOrfStats2:</TD><TD>Collect stats on refSeq cDNAs aligned to another
species via axtForEst</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>twinOrfStats3:</TD><TD>Collect stats on refSeq cDNAs aligned to another
species via axtForEst</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>twoBitInfo:</TD><TD>get information about sequences in a .2bit file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>twoBitMask:</TD><TD>apply masking to a .2bit file, creating a new .2bit file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>twoBitToFa:</TD><TD>Convert all or part of .2bit file to fasta</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txAbFragFind:</TD><TD>Search database for what are probably antibody fragments.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txBedToGraph:</TD><TD>Cluster together beds from txPslToBed. Make transcript graphs out of clusters.
txBedToGraph in1.bed in1Type [in2.bed in2type ...]  out.txg
options:</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsBadBed:</TD><TD>Create a bed file with regions that don't really have CDS, but
that might look like it.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsCluster:</TD><TD>Cluster transcripts purely in the CDS regions, only putting things
together if they share same frame as well as a genomic region.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsEvFromBed:</TD><TD>Make a cds evidence file (.tce) from an existing bed file.  Used mostly
in transferring CCDS coding regions currently.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsEvFromBorf:</TD><TD>Convert borfBig format to txCdsEvidence (tce) in an effort
to annotate the coding regions.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsEvFromProtein:</TD><TD>Convert transcript/protein alignments and other evidence
into a transcript CDS evidence (tce) file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsEvFromRna:</TD><TD>Convert transcript/rna alignments, genbank CDS file, and
other info to transcript CDS evidence (tce) file.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsGoodBed:</TD><TD>Create positive example training set for SVM. This is
based on the refSeq reviewed genes, but we fragment a certain percentage
of them so as not to end up with a SVM that *requires* a complete </TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsOrfInfo:</TD><TD>Given a sequence and a putative ORF, calculate some basic information on it.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsOrtho:</TD><TD>Figure out how CDS looks in other organisms.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsPick:</TD><TD>Pick best CDS if any for transcript given evidence.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsPredict:</TD><TD>Somewhat simple-minded ORF predictor using a weighting scheme.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsRaExceptions:</TD><TD>Mine exceptional things like selenocysteine out of genbank ra file.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsRefBestEvOnly:</TD><TD>Go through a cdsEvidence file, and extract only the bits that refer to the native orf for a RefSeqReviewed transcript.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsRepick:</TD><TD>OBSOLETE program. The scheme this implemented ended up
not working so well. It's still in the source tree because it may contain
some useful routines for other programs</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsSuspect:</TD><TD>Flag cases where the CDS prediction is very suspicious, including
CDSs that lie entirely in an intron or in the 3' UTR of another, better looking
transcript.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsSvmInput:</TD><TD>Create input for svm_light, a nice support vector machine classifier.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsToGene:</TD><TD>Convert transcript bed and best cdsEvidence to genePred and
protein sequence.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txCdsWeed:</TD><TD>Remove bad CDSs including NMD candidates</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneAccession:</TD><TD>Assign permanent accession number to genes.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneAlias:</TD><TD>Make kgAlias and kgProtAlias tables.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneAltProt:</TD><TD>Figure out statistics on number of alternative proteins produced by alt-splicing.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneCanonical:</TD><TD>Pick a canonical version of each gene - that is the form
to use when just interested in a single splicing varient. Produces final
transcript clusters as well.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneCdsMap:</TD><TD>Create mapping between CDS region of gene and genome.
This is used to build the exon track in the proteome browser.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneColor:</TD><TD>Figure out color to draw gene in.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneExplainUpdate1:</TD><TD>Make table explaining correspondence between older known genes
and ucsc genes.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneFromBed:</TD><TD>Convert from bed to knownGenes format table (genePred + uniProt ID)</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneProtAndRna:</TD><TD>Create fasta files with our proteins and transcripts.
These echo RefSeq when gene is based on RefSeq. Otherwise they are taken from
the genome.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneSeparateNoncoding:</TD><TD>Separate genes into four piles - coding, non-coding that overlap coding, and independent non-coding.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txGeneXref:</TD><TD>Make kgXref type table for genes.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txInfoAssemble:</TD><TD>Assemble information from various sources into txInfo table.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>txOrtho:</TD><TD>Produce list of shared edges between two transcription graphs in two species.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txPslFilter:</TD><TD>Do rna/rna filter.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txPslToBed:</TD><TD>txPsltoBed - Convert a psl to a bed file by projecting it onto its target
sequence. Optionally merge adjacent blocks and trim to splice sites.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txReadRa:</TD><TD>Read ra files from genbank and parse out relevant info into some tab-separated files.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txWalk:</TD><TD>Walk transcription graph and output transcripts.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txgAddEvidence:</TD><TD>Add evidence from a bed file to existing transcript graph.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>txgAnalyze:</TD><TD>Analyse transcription graph for alt exons, alt 3', alt 5',
retained introns, alternative promoters, etc.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txgGoodEdges:</TD><TD>Get edges that are above a certain threshold.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txgToAgx:</TD><TD>Convert from txg (txGraph) format to agx (altGraphX)</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txgToXml:</TD><TD>Convert txg to an XML format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>txgTrim:</TD><TD>Trim out parts of txGraph that are not of sufficient weight.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>udcCleanup:</TD><TD>Clean up old unused files in udcCache.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>undupFa:</TD><TD>rename duplicate records in FA file
usage
undupFa faFile(s)</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>upper:</TD><TD>strip numbers, spaces, and punctuation turn to upper case</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>utrFa:</TD><TD>Get UTRs as fasta files</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>validateFiles:</TD><TD>Validate format of different track input files
Program exits with non-zero status if any errors detected
otherwise exits with zero status</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>venn:</TD><TD>Do venn diagram calculations</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>wabToSt:</TD><TD>Convert WABA output to something Intronerator understands better</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>weedLines:</TD><TD>Selectively remove lines from file</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>whyConserved:</TD><TD>Try and analyse why a particular thing is conserved</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>wigEncode:</TD><TD>convert Wiggle ascii data to binary format</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>wigTestMaker:</TD><TD>Create test wig files.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>wigToBigWig:</TD><TD>Convert ascii format wig file (in fixedStep, variableStep or bedGraph
format) to binary big wig format.</TD></TR>
<TR><TD VALIGN=TOP ALIGN=LEFT>wordLine:</TD><TD>chop up words by white space and output them with one
word to each line.</TD></TR>
 
<TR><TD VALIGN=TOP ALIGN=LEFT>xmlCat:</TD><TD>Concatenate xml files together, stuffing all records inside a single outer tag. </TD></TR>
<TR><TD VALIGN=TOP 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>
 


[[Category:Technical FAQ]]
[[Category:Technical FAQ]]

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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