Generic

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
raSqlQuery
Function: Do a SQL-like query on a RA file
Usage: raSqlQuery raFile(s) query-options
bedToPsl
Function: Convert bed format files to psl format
Usage: bedToPsl chromSizes bedFile pslFile
blastToPsl
Function: Convert blast alignments to PSLs.
Usage: blastToPsl [options] blastOutput psl
faRc
Function: Reverse complement a FA file
Usage: faRc in.fa out.fa
htmlCheck
Function: htmlCheck - Do a little reading and verification of html file
Usage: htmlCheck how url
ave
Function: Compute average and basic stats
Usage: ave file
axtSort
Function: Sort axt files
Usage: axtSort in.axt out.axt
subColumn
Function: Substitute one column in a tab-separated file.
Usage: subColumn column in.tab sub.tab out.tab
tailLines
Function: Add tail to each line of file
Usage: tailLines file tail
axtToPsl
Function: Convert axt to psl format
Usage: axtToPsl in.axt tSizes qSizes out.psl
bedPileUps
Function: Find (exact) overlaps if any in bed input
Usage: bedPileUps in.bed
blastXmlToPsl
Function: Convert blast XML output to PSLs
Usage: blastXmlToPsl [options] blastXml psl
estOrient
Function: Convert ESTs so that orientation matches directory of transcription
Usage: estOrient [options] db estTable outPsl
liftUp
Function: Change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf.bscore .tab .gdup .axt .chain .net, genePred, .wab, .bed, or .bed8 files toparent coordinate system.
Usage: liftUp [-type=.xxx] destFile liftSpec how sourceFile(s)