Generic

Function: Convert PSL to human readable output

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

Function: Add noise to fasta file

Usage: faNoise inName outName transitionPpt transversionPpt insertPpt deletePpt chimeraPpt

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

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

Function: Chop up words by white space and output them with oneword to each line.

Usage: wordLine inFile(s)

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

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

Function: Convert chromGraph binary to ascii format.

Usage: chromGraphFromBin in.chromGraph out.tab

Function: Count the number of occurences of a particular char

Usage: countChars char file(s)

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)

Function: Convert file to C strings

Usage: stringify [options] in.txt

Function: Get poly A sizes

Usage: faPolyASizes in.fa out.tab

Function: Print size of nibs

Usage: nibSize nib1 [...]

Function: Collect counts on PSL alignments for making histograms.

Usage: pslHisto [options] what inPsl outHisto

Function: Make a histogram in ascii

Usage: textHistogram [options] inFile

Function: Create trackDb table from text files.Note that the browser supports multiple trackDb tables, usuallyin the form: trackDb_YourUserName. Which particular trackDbtable the browser uses is specified in the hg.conf file foundeither in your home directory file '.hg.conf' or in the web server'scgi-bin/hg.conf configuration file with the setting: db.trackDb=trackDbsee also: src/product/ex.hg.conf discussion of this setting.

Usage: hgTrackDb [options] org database trackDb trackDb.sql hgRoot

Function: Substitute one character for another throughout a file.

Usage: subChar oldChar newChar file(s)