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Function: Convert bed format files to psl format
Usage: bedToPsl chromSizes bedFile pslFile
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Function: Find perfect matches in sequence.
Usage: oligoMatch oligos sequence output.bed
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Function: Convert chromGraph binary to ascii format.
Usage: chromGraphFromBin in.chromGraph out.tab
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Function: Collect counts on PSL alignments for making histograms.
Usage: pslHisto [options] what inPsl outHisto
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Function: Concatenate xml files together, stuffing all records inside a single outer tag.
Usage: xmlCat XXX
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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: Convert blast alignments to PSLs.
Usage: blastToPsl [options] blastOutput psl
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Function: Sort chains. By default sorts by score.Note this loads all chains into memory, so it is notsuitable for large sets. Instead, run chainSort onmultiple small files, followed by chainMergeSort.
Usage: chainSort inFile outFile
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Function: This script sort clusters in .clstr file by length, size
Usage: Clstr_sort_by.pl input.clstr no > input_sort.clstr
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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: Convert blastz lav to psl format
Usage: lavToPsl in.lav out.psl
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Function: Filter out parts of net. What passesfilter goes to standard output. Note a net is arecursive data structure. If a parent fails to passthe filter, the children are not even considered.
Usage: netFilter in.net(s)
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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: 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: Get rid of chains that are primarily the results of repeats and degenerate DNA
Usage: chainAntiRepeat tNibDir qNibDir inChain outChain