Generic

Function: Convert bed format files to psl format

Usage: bedToPsl chromSizes bedFile pslFile

Function: htmlCheck - Do a little reading and verification of html file

Usage: htmlCheck how url

Function: Convert blast alignments to PSLs.

Usage: blastToPsl [options] blastOutput psl

Function: Reverse complement a FA file

Usage: faRc in.fa out.fa

Function: Sort axt files

Usage: axtSort in.axt out.axt

Function: Add tail to each line of file

Usage: tailLines file tail

Function: Calculate inner distance between read pairs.

Usage: inner_distance.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output -r hg19.refseq.bed12

Function: Do a SQL-like query on a RA file

Usage: raSqlQuery raFile(s) query-options

Function: Compute average and basic stats

Usage: ave file

Function: Find (exact) overlaps if any in bed input

Usage: bedPileUps in.bed

Function: Substitute one column in a tab-separated file.

Usage: subColumn column in.tab sub.tab out.tab

Function: Convert axt to psl format

Usage: axtToPsl in.axt tSizes qSizes out.psl

Function: Convert blast XML output to PSLs

Usage: blastXmlToPsl [options] blastXml psl

Function: Create a psl of fake-mRNA aligned to gene-preds from a file or table.

Usage: genePredToFakePsl db fileTbl pslOut cdsOut

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)