Generic

pslSort
Function: Merge and sort psCluster .psl output files
Usage: pslSort dirs[1|2] outFile tempDir inDir(s)
checkTableCoords
Function: Check invariants on genomic coords in table(s).
Usage: checkTableCoords database [tableName]
faToFastq
Function: Convert fa to fastq format, just faking quality values.
Usage: faToFastq in.fa out.fastq
subChar
Function: Substitute one character for another throughout a file.
Usage: subChar oldChar newChar file(s)
hgTrackDb
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
newProg
Function: Make a new C source skeleton.
Usage: newProg progName description words
bedRestrictToPositions
Function: Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file.
Usage: bedRestrictToPositions in.bed restrict.bed out.bed
trfBig
Function: Mask tandem repeats on a big sequence file.
Usage: trfBig inFile outFile
gapToLift
Function: Create lift file from gap table(s)
Usage: gapToLift [options] db liftFile.lft
pslMrnaCover
Function: Make histogram of coverage percentage of mRNA in psl.
Usage: pslMrnaCover mrna.psl mrna.fa
htmlCheck
Function: htmlCheck - Do a little reading and verification of html file
Usage: htmlCheck how url
bedToPsl
Function: Convert bed format files to psl format
Usage: bedToPsl chromSizes bedFile pslFile
chainSort
Function: Sort chains. By default sorts by score.Note this loads all chains into memory, so it is notsuitable for large sets. Instead, run chainSort onmultiple small files, followed by chainMergeSort.
Usage: chainSort inFile outFile
clstr_merge_noorder.pl
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
tailLines
Function: Add tail to each line of file
Usage: tailLines file tail