Generic

Function: htmlCheck - Do a little reading and verification of html file

Usage: htmlCheck how url

Function: Convert axt to psl format

Usage: axtToPsl in.axt tSizes qSizes out.psl

Function: It merges two or more .clstr files. The cluster orders do not have to be identical.

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

Function: Reverse complement a FA file

Usage: faRc in.fa out.fa

Function: Convert from compressed to uncompressedquality score format.

Usage: qacToQa in.qac out.qa

Function: Make histogram of coverage percentage of mRNA in psl.

Usage: pslMrnaCover mrna.psl mrna.fa

Function: Make a new C source skeleton.

Usage: newProg progName description words

Function: Substitute one column in a tab-separated file.

Usage: subColumn column in.tab sub.tab out.tab

Function: Convert blast alignments to PSLs.

Usage: blastToPsl [options] blastOutput psl

Function: Find (exact) overlaps if any in bed input

Usage: bedPileUps in.bed

Function: Add tail to each line of file

Usage: tailLines file tail

Function: Change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf.bscore .tab .gdup .axt .chain .net, genePred, .wab, .bed, or .bed8 files toparent coordinate system.

Usage: liftUp [-type=.xxx] destFile liftSpec how sourceFile(s)

Function: Sort axt files

Usage: axtSort in.axt out.axt

Function: Convert blast XML output to PSLs

Usage: blastXmlToPsl [options] blastXml psl

Function: Create a psl of fake-mRNA aligned to gene-preds from a file or table.

Usage: genePredToFakePsl db fileTbl pslOut cdsOut