Generic

Function: Get rid of chains that are primarily the results of repeats and degenerate DNA

Usage: chainAntiRepeat tNibDir qNibDir inChain outChain

Function: Find perfect matches in sequence.

Usage: oligoMatch oligos sequence output.bed

Function: Convert blastz lav to psl format

Usage: lavToPsl in.lav out.psl

Function: Convert unix timestamp to date string

Usage: gmtime

Function: Get data for generating histograms from a genePred file.

Usage: genePredHisto [options] what genePredFile histoOut

Function: Concatenate xml files together, stuffing all records inside a single outer tag.

Usage: xmlCat XXX

Function: Try to fetch url with multiple connections

Usage: paraFetch N R URL {outPath}

Function: Map PSLs alignments to new targets using alignments ofthe old target to the new target. Given inPsl and mapPsl, wherethe target of inPsl is the query of mapPsl, create a new PSLwith the query of inPsl aligned to all the targets of mapPsl.If inPsl is a protein to nucleotide alignment and mapPsl is anucleotide to nucleotide alignment, the resulting alignment isnucleotide to nucleotide alignment of a hypothetical mRNA thatwould code for the protein. This is useful as it gives basealignments of spliced codons. A chain file may be used insteadmapPsl.

Usage: pslMap [options] inPsl mapFile outPsl

Function: Combine sorted files into larger sorted file

Usage: chainMergeSort file(s)

Function: Load a wiggle track definition into database

Usage: hgLoadWiggle [options] database track files(s).wig

Function: Concatenate psl files

Usage: pslCat file(s)

Function: Remove duplicate records in FA file

Usage: rmFaDup oldName.fa newName.fa

Function: Drop tables from a database older than specified N hours

Usage: dbTrash -age=N [-drop] [-historyToo] [-db=<DB>] [-verbose=N]

Function: It merges two or more .clstr files. The cluster orders need to be identical.

Usage: clstr_merge.pl db2new.clstr db3new.clstr > db23new.clstr

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

Usage: wordLine inFile(s)