Generic

bedGeneParts
Function: Given a bed, spit out promoter, first exon, or all introns.
Usage: bedGeneParts part in.bed out.bed
pslLiftSubrangeBlat
Function: Lift PSLs from blat subrange alignments
Usage: pslLiftSubrangeBlat isPsl outPsl
gff3ToPsl
Function: Convert a GFF3 CIGAR file to a PSL file
Usage: gff3ToPsl mapFile inGff3 out.psl
pslDropOverlap
Function: Deletes all overlapping self alignments.
Usage: pslDropOverlap in.psl out.psl
raToTab
Function: Convert ra file to table.
Usage: raToTab in.ra out.tab
calc
Function: Little command line calculator
Usage: calc this + that * theOther / (a + b)
sizeof
Function: Show size of various C types for reference
Usage: sizeof
autoDtd
Function: Give this a XML document to look at and it will come up with a DTDto describe it.
Usage: autoDtd in.xml out.dtd out.stats
pslToBed
Function: pslToBed: tranform a psl format file to a bed format file.
Usage: pslToBed psl bed
toUpper
Function: Convert lower case to upper case in file. Leave other chars alone
Usage: toUpper inFile outFile
netSplit
Function: Split a genome net file into chromosome net files
Usage: netSplit in.net outDir
chainAntiRepeat
Function: Get rid of chains that are primarily the results of repeats and degenerate DNA
Usage: chainAntiRepeat tNibDir qNibDir inChain outChain
genePredCheck
Function: Validate genePred files or tables
Usage: genePredCheck [options] fileTbl ..
validateFiles
Function: 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
Usage: validateFiles -chromInfo=FILE -options -type=FILE_TYPE file1 [file2 [...]]
lavToPsl
Function: Convert blastz lav to psl format
Usage: lavToPsl in.lav out.psl