Generic

Function: Convert fa to fastq format, just faking quality values.

Usage: faToFastq in.fa out.fastq

Function: Substitute one character for another throughout a file.

Usage: subChar oldChar newChar file(s)

Function: Load a generic bed file into database

Usage: hgLoadBed database track files(s).bed

Function: Mask tandem repeats on a big sequence file.

Usage: trfBig inFile outFile

Function: Find common patterns in DNA

Usage: ameme good=goodIn.fa [bad=badIn.fa] [numMotifs=2] [background=m1] [maxOcc=2] [motifOutput=fileName] [html=output.html] [gif=output.gif] [rcToo=on] [controlRun=on] [startScanLimit=20] [outputLogo] [constrainer=1]

Function: Check invariants on genomic coords in table(s).

Usage: checkTableCoords database [tableName]

Function: Make a new C source skeleton.

Usage: newProg progName description words

Function: Merge and sort psCluster .psl output files

Usage: pslSort dirs[1|2] outFile tempDir inDir(s)

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

Function: Create lift file from gap table(s)

Usage: gapToLift [options] db liftFile.lft

Function: Swap target and query in chain

Usage: chainSwap in.chain out.chain

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: Convert from compressed to uncompressedquality score format.

Usage: qacToQa in.qac out.qa

Function: Convert bed format files to psl format

Usage: bedToPsl chromSizes bedFile pslFile

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