Software Usage Function
netChainSubset netChainSubset in.chain out.chain Create chain file with subset of chains that appear in the net
faSplit faSplit how input.fa count outRoot Split an fa file into several files.
faCount faCount file(s).fa Count base statistics and CpGs in fasta files.
fastqToFa fastqToFa [options] in.fastq out.fa Convert from fastq to fasta format.
stringify stringify [options] in.txt Convert file to C strings
tickToDate tickToDate ticks Convert seconds since 1970 to time and date
chainMergeSort chainMergeSort file(s) Combine sorted files into larger sorted file
pslStats pslStats [options] psl statsOut Collect statistics from a psl file.
toUpper toUpper inFile outFile Convert lower case to upper case in file. Leave other chars alone
wordLine wordLine inFile(s) Chop up words by white space and output them with oneword to each line.
bedToBigBed bedToBigBed in.bed chrom.sizes Convert bed file to bigBed.
hgLoadOut hgLoadOut database file(s).out Load RepeatMasker .out files into database
netToAxt netToAxt in.chain target.2bit query.2bit out.axt Convert net (and chain) to axt.
pslDropOverlap pslDropOverlap in.psl out.psl Deletes all overlapping self alignments.
validateManifest validateManifest Validates the ENCODE3 manifest.txt file. Calls validateFiles on each file in the manifest.Exits with a zero status for no errors detected and non-zero for errors. Writes Error messages to stderr
autoDtd autoDtd in.xml out.dtd out.stats Give this a XML document to look at and it will come up with a DTDto describe it. db2new.clstr db3new.clstr > db23new.clstr It merges two or more .clstr files. The cluster orders need to be identical.
tdbQuery tdbQuery sqlStatement Query the trackDb system using SQL syntax.
validateFiles validateFiles -chromInfo=FILE -options -type=FILE_TYPE file1 [file2 [...]] Validates the format of different genomic files.Exits with a zero status for no errors detected and non-zero for errors.Uses filename 'stdin' to read from stdin.Automatically decompresses Files in .gz, .bz2, .zip, .Z format.Accepts multiple input files of the same type.Writes Error messages to stderr
newProg newProg progName description words Make a new C source skeleton.