Generic

Function: Make a histogram in ascii

Usage: textHistogram [options] inFile

Function: Create a sequence dictionary file from a fasta file.

Usage: samtools dict <ref.fasta|ref.fasta.gz>

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]

Function: Swap target and query in chain

Usage: chainSwap in.chain out.chain

Function: Get poly A sizes

Usage: faPolyASizes in.fa out.tab

Function: Collect statistics from a psl file.

Usage: pslStats [options] psl statsOut

Function: Add noise to fasta file

Usage: faNoise inName outName transitionPpt transversionPpt insertPpt deletePpt chimeraPpt

Function: Convert PSL to human readable output

Usage: pslPretty in.psl target.lst query.lst pretty.out

Function: Remove duplicate records in FA file

Usage: rmFaDup oldName.fa newName.fa

Function: Collect counts on PSL alignments for making histograms.

Usage: pslHisto [options] what inPsl outHisto

Function: Combine sorted files into larger sorted file

Usage: chainMergeSort file(s)

Function: Convert chromGraph binary to ascii format.

Usage: chromGraphFromBin in.chromGraph out.tab

Function: Convert from psl to pslx format, which includes sequences

Usage: pslToPslx [options] in.psl qSeqSpec tSeqSpec out.pslx

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

Function: Print size of nibs

Usage: nibSize nib1 [...]