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