Software Usage Function
blastToPsl blastToPsl [options] blastOutput psl Convert blast alignments to PSLs.
trfBig trfBig inFile outFile Mask tandem repeats on a big sequence file.
samtools faidx samtools faidx <ref.fasta> [region1 [...]] Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk. If regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format.
pslHisto pslHisto [options] what inPsl outHisto Collect counts on PSL alignments for making histograms.
faPolyASizes faPolyASizes in.fa Get poly A sizes
pslMrnaCover pslMrnaCover mrna.psl mrna.fa Make histogram of coverage percentage of mRNA in psl.
subChar subChar oldChar newChar file(s) Substitute one character for another throughout a file.
wigToBigWig wigToBigWig in.wig chrom.sizes Convert ascii format wig file (in fixedStep, variableStepor bedGraph format) to binary bigwig format.
oligoMatch oligoMatch oligos sequence output.bed Find perfect matches in sequence.
pslToPslx pslToPslx [options] in.psl qSeqSpec tSeqSpec out.pslx Convert from psl to pslx format, which includes sequences db2new.clstr db3new.clstr > db23new.clstr It merges two or more .clstr files. The cluster orders do not have to be identical.
xmlCat xmlCat XXX Concatenate xml files together, stuffing all records inside a single outer tag.
netFilter netFilter 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.
ameme 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] Find common patterns in DNA
chainAntiRepeat chainAntiRepeat tNibDir qNibDir inChain outChain Get rid of chains that are primarily the results of repeats and degenerate DNA input.clstr no > input_sort.clstr This script sort clusters in .clstr file by length, size
bedCoverage bedCoverage database bedFile Analyse coverage by bed files - chromosome bychromosome and genome-wide
genePredToFakePsl genePredToFakePsl db fileTbl pslOut cdsOut Create a psl of fake-mRNA aligned to gene-preds from a file or table.
hgLoadWiggle hgLoadWiggle [options] database track files(s).wig Load a wiggle track definition into database
ave ave file Compute average and basic stats