KnownGenesToBed

##Motivation

converts UCSC knownGenes file to BED.

##Compilation

See also Compilation.

$ make kg2bed

##Synopsis

$ java -jar dist/kg2bed.jar (stdin|file) 

##Options

Option	Description
-i	don't print introns
-u	don't print utr
-c	don't print cds
-x	don't print exons
-t	don't print transcripts
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/KnownGenesToBed.java

##Example

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" |\
  gunzip -c |\
  java -jar dist/kg2bed.jar
chr1	11873	14409	+	uc001aaa.3	TRANSCRIPT	uc001aaa.3
chr1	11873	12227	+	uc001aaa.3	EXON	Exon 1
chr1	12227	12612	+	uc001aaa.3	INTRON	Intron 1
chr1	11873	12227	+	uc001aaa.3	UTR	UTR3
chr1	12612	12721	+	uc001aaa.3	EXON	Exon 2
chr1	12721	13220	+	uc001aaa.3	INTRON	Intron 2
chr1	12612	12721	+	uc001aaa.3	UTR	UTR3
chr1	13220	14409	+	uc001aaa.3	EXON	Exon 3
chr1	13220	14409	+	uc001aaa.3	UTR	UTR3
chr1	11873	14409	+	uc010nxr.1	TRANSCRIPT	uc010nxr.1
chr1	11873	12227	+	uc010nxr.1	EXON	Exon 1
chr1	12227	12645	+	uc010nxr.1	INTRON	Intron 1
chr1	11873	12227	+	uc010nxr.1	UTR	UTR3
chr1	12645	12697	+	uc010nxr.1	EXON	Exon 2
chr1	12697	13220	+	uc010nxr.1	INTRON	Intron 2

##See also

• https://www.biostars.org/p/151628

##History

• 2014: Creation
• 2015-07-21 : removed duplicate exon

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.