Generic

Function: Filter cDNA alignments in psl format

Usage: pslCDnaFilter [options] inPsl outPsl

Function: Select records based on overlapping chromosome ranges

Usage: overlapSelect [options] selectFile inFile outFile

Function: Get rid of sequences with too many N's

Usage: faFilterN in.fa out.fa maxPercentN

Function: Convert Wiggle ascii data to binary format

Usage: wigEncode [options] wigInput wigFile wibFile

Function: catDir - concatenate files in directory to stdout.For those times when too many files for cat to handle.

Usage: catDir dir(s)

Function: catUncomment - Concatenate input removing lines that start with '#'Output goes to stdout

Usage: catUncomment file(s)

Function: Produce a masked .fa file given an unmasked .fa anda RepeatMasker .out file, or a .bed file to mask on.

Usage: maskOutFa in.fa maskFile out.fa.masked

Function: Remove chains that don't have a chance of being netted

Usage: chainPreNet in.chain target.sizes query.sizes out.chain

Function: Test and describe search specs in hgFindSpec tables.

Usage: checkHgFindSpec database [options | termToSearch]

Function: Execute mysqldump using passwords from .hg.conf

Usage: hgsqldump [OPTIONS] database [tables]

Function: Create single-coverage genePred files

Usage: genePredSingleCover [options] inGenePred outGenePred

Function: Analyse repeats and generate genome wide bestalignments from a sorted set of local alignments

Usage: pslReps in.psl out.psl out.psr

Function: Convert from chain to axt file

Usage: chainToAxt in.chain tNibDirOr2bit qNibDirOr2bit out.axt

Function: colTransform - Add and/or multiply column by constant.

Usage: colTransform column input.tab addFactor mulFactor output.tab

Function: Intersect two bed files

Usage: bedIntersect a.bed b.bed output.bed