Generic

ameme
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]
chainSwap
Function: Swap target and query in chain
Usage: chainSwap in.chain out.chain
axtSort
Function: Sort axt files
Usage: axtSort in.axt out.axt
blastToPsl
Function: Convert blast alignments to PSLs.
Usage: blastToPsl [options] blastOutput psl
qacToQa
Function: Convert from compressed to uncompressedquality score format.
Usage: qacToQa in.qac out.qa
raSqlQuery
Function: Do a SQL-like query on a RA file
Usage: raSqlQuery raFile(s) query-options
inner_distance.py
Function: Calculate inner distance between read pairs.
Usage: inner_distance.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output -r hg19.refseq.bed12
faRc
Function: Reverse complement a FA file
Usage: faRc in.fa out.fa
ave
Function: Compute average and basic stats
Usage: ave file
bedPileUps
Function: Find (exact) overlaps if any in bed input
Usage: bedPileUps in.bed
subColumn
Function: Substitute one column in a tab-separated file.
Usage: subColumn column in.tab sub.tab out.tab
genePredToFakePsl
Function: Create a psl of fake-mRNA aligned to gene-preds from a file or table.
Usage: genePredToFakePsl db fileTbl pslOut cdsOut
paraSync
Function: paraSync 1.0paraSync - uses paraFetch to recursively mirror url to given path
Usage: paraSync {options} N R URL outPath
estOrient
Function: Convert ESTs so that orientation matches directory of transcription
Usage: estOrient [options] db estTable outPsl
blastXmlToPsl
Function: Convert blast XML output to PSLs
Usage: blastXmlToPsl [options] blastXml psl