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Function: Print size of nibs
Usage: nibSize nib1 [...]
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Function: Substitute one character for another throughout a file.
Usage: subChar oldChar newChar file(s)
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Function: Mask tandem repeats on a big sequence file.
Usage: trfBig inFile outFile
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Function: Convert fa to fastq format, just faking quality values.
Usage: faToFastq in.fa out.fastq
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Function: Merge and sort psCluster .psl output files
Usage: pslSort dirs[1|2] outFile tempDir inDir(s)
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Function: 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]
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Function: Check invariants on genomic coords in table(s).
Usage: checkTableCoords database [tableName]
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Function: Create lift file from gap table(s)
Usage: gapToLift [options] db liftFile.lft
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Function: Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file.
Usage: bedRestrictToPositions in.bed restrict.bed out.bed
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Function: Make a new C source skeleton.
Usage: newProg progName description words
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Function: It merges two or more .clstr files. The cluster orders do not have to be identical.
Usage: clstr_merge_noorder.pl db2new.clstr db3new.clstr > db23new.clstr
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Function: Swap target and query in chain
Usage: chainSwap in.chain out.chain
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Function: Make histogram of coverage percentage of mRNA in psl.
Usage: pslMrnaCover mrna.psl mrna.fa
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Function: Convert from compressed to uncompressedquality score format.
Usage: qacToQa in.qac out.qa
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Function: Convert bed format files to psl format
Usage: bedToPsl chromSizes bedFile pslFile