Generic

Function: Return all *but* the first N lines of a file.

Usage: headRest count fileName

Function: It combines a .clstr file with its parent .clstr file

Usage: clstr_rev.pl nr90.clstr nr60.clstr > nr60_from90.clstr

Function: Intersect two bed files

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

Function: Convert PSL alignments of mRNAs to gene annotations

Usage: mrnaToGene [options] psl genePredFile

Function: Convert from compressed quality score format to wiggle format.

Usage: qacToWig in.qac outFileOrDir

Function: Convert seconds since 1970 to time and date

Usage: tickToDate ticks

Function: Convert between textual and numeric flag representation.

Usage: samtools flags INT|STR[,...]

Function: Generate structures code and parser for XML file from DTD-like spec

Usage: autoXml file.dtdx root

Function: Show information about a bigBed file.

Usage: bigBedInfo file.bb

Function: Query the trackDb system using SQL syntax.

Usage: tdbQuery sqlStatement

Function: Create indices for simple line-oriented file of format<symbol> <free text>

Usage: ixIxx in.text out.ix out.ixx

Function: Program to create random fasta records

Usage: faRandomize [-seed=N] in.fa randomized.fa

Function: Convert from uncompressed to compressedquality score format.

Usage: qaToQac in.qa out.qac

Function: Load RepeatMasker .out files into database

Usage: hgLoadOut database file(s).out

Function: Given a bed, spit out promoter, first exon, or all introns.

Usage: bedGeneParts part in.bed out.bed