Generic

Function: Search a crTree indexed bed file and print all items that overlap query.

Usage: crTreeSearchBed file.bed index.cr chrom start end

Function: Get rid of sequences with too many N's

Usage: faFilterN in.fa out.fa maxPercentN

Function: Convert unix timestamp to date string

Usage: localtime

Function: Split up a file

Usage: splitFile source linesPerFile outBaseName

Function: Return all *but* the first N lines of a file.

Usage: headRest count fileName

Function: Count number of times a base is overlapped by theitems in a bed file. Output is bedGraph 4 to stdout.

Usage: sort bedFile.bed | bedItemOverlapCount [options] <database> stdin

Function: Take a .agp file and .fa file and ensure that they are in synch

Usage: checkAgpAndFa in.agp in.fa

Function: Read in FA file with long lines and rewrite it with shorter lines

Usage: chopFaLines in.fa out.fa

Function: Split chains up by target or query sequence

Usage: chainSplit outDir inChain(s)

Function: Split PSL files into non-overlapping sets

Usage: pslPartition [options] pslFile outDircreated under outDir to prevent slow access to huge directories.

Function: Convert from chain to axt file

Usage: chainToAxt in.chain tNibDirOr2bit qNibDirOr2bit out.axt

Function: Dump out all or part of a relational database to XML, guidedby a dump specification. See sqlToXml.doc for additional information.

Usage: sqlToXml database dumpSpec.od output.xml

Function: Create chain file with subset of chains that appear in the net

Usage: netChainSubset in.net in.chain out.chain

Function: Produce an overview of a database.

Usage: dbSnoop database output

Function: Convert PSL alignments of mRNAs to gene annotations

Usage: mrnaToGene [options] psl genePredFile