Custom Track Examples

Return to CGI testing: http://genomewiki.ucsc.edu/index.php/CGI_Testing

All examples below can be pasted directly into the custom tracks input menu.

RGB Item Example

browser position chr7:127471196-127495720
browser hide all
track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 itemRgb="On"
chr7    127471196       127472363       Pos1    0       +       127471196       127472363       255,0,0
chr7    127472363       127473530       Pos2    0       +       127472363       127473530       255,0,0
chr7    127473530       127474697       Pos3    0       +       127473530       127474697       255,0,0
chr7    127474697       127475864       Pos4    0       +       127474697       127475864       255,0,0
chr7    127475864       127477031       Neg1    0       -       127475864       127477031       0,0,255
chr7    127477031       127478198       Neg2    0       -       127477031       127478198       0,0,255
chr7    127478198       127479365       Neg3    0       -       127478198       127479365       0,0,255
chr7    127479365       127480532       Pos5    0       +       127479365       127480532       255,0,0
chr7    127480532       127481699       Neg4    0       -       127480532       127481699       0,0,255

Big Bed Example

track type=bigBed name="bigBed Example" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/bigBedExample.bb
browser position chr21:33,031,597-33,041,570

BedGraph Example

browser position chr19:59302001-59304701
track type=bedGraph name="BedGraph Format Example" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
chr19 59302000 59302300 -1.0
chr19 59302300 59302600 -0.75
chr19 59302600 59302900 -0.50
chr19 59302900 59303200 -0.25
chr19 59303200 59303500 0.0
chr19 59303500 59303800 0.25
chr19 59303800 59304100 0.50
chr19 59304100 59304400 0.75
chr19 59304400 59304700 1.00

Variable Step Example

browser position chr19:59304200-59310700
browser hide all
track type=wiggle_0 name="variableStep" description="variableStep format" visibility=full autoScale=off viewLimits=0.0:25.0 color=50,150,255 yLineMark=11.76 yLineOnOff=on priority=10
variableStep chrom=chr19 span=150
59304701 10.0
59304901 12.5
59305401 15.0
59305601 17.5
59305901 20.0
59306081 17.5
59306301 15.0
59306691 12.5
59307871 10.0

Fixed Step Example

track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 graphType=points priority=20
fixedStep chrom=chr19 start=59307401 step=300 span=200
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MAF Example

track name=euArc visibility=pack
##maf version=1 scoring=tba.v8 
# tba.v8 (((human chimp) baboon) (mouse rat)) 

a score=23262.0
s hg18.chr7    27578828 38 + 158545518 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG
s panTro1.chr6 28741140 38 + 161576975 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG
s baboon         116834 38 +   4622798 AAA-GGGAATGTTAACCAAATGA---GTTGTCTCTTATGGTG
s mm4.chr6     53215344 38 + 151104725 -AATGGGAATGTTAAGCAAACGA---ATTGTCTCTCAGTGTG
s rn3.chr4     81344243 40 + 187371129 -AA-GGGGATGCTAAGCCAATGAGTTGTTGTCTCTCAATGTG

a score=5062.0
s hg18.chr7    27699739 6 + 158545518 TAAAGA
s panTro1.chr6 28862317 6 + 161576975 TAAAGA
s baboon         241163 6 +   4622798 TAAAGA
s mm4.chr6     53303881 6 + 151104725 TAAAGA
s rn3.chr4     81444246 6 + 187371129 taagga

a score=6636.0
s hg18.chr7    27707221 13 + 158545518 gcagctgaaaaca
s panTro1.chr6 28869787 13 + 161576975 gcagctgaaaaca
s baboon         249182 13 +   4622798 gcagctgaaaaca
s mm4.chr6     53310102 13 + 151104725 ACAGCTGAAAATA

BAM Example

track type=bam name="BAM Example One" description="Bam Ex. 1: 1000 Genomes read alignments (individual NA12878)" pairEndsByName=. pairSearchRange=10000 chromosomes=chr21 bamColorMode=gray maxWindowToDraw=200000 db=hg18 visibility=pack bigDataUrl=http://hgwdev.cse.ucsc.edu/goldenPath/help/examples/bamExample.bam
browser position chr21:33,038,946-33,039,092

Other Examples

##Example 6 from Custom Annotation Tracks User's Guide
browser position chr22:13073000-13074000
browser hide all
track name=fishBlats description="Fish BLAT" visibility=2 useScore=1
59 9 0 0 1 823 1 96 +- FS_CONTIG_48080_1 1955 171 1062 chr22 47748585 13073589 13073753 2 48,20,  171,1042,  34674832,34674976,
59 7 0 0 1 55 1 55 +- FS_CONTIG_26780_1 2825 2456 2577 chr22 47748585 13073626 13073747 2 21,45,  2456,2532,  34674838,34674914,
59 7 0 0 1 55 1 55 -+ FS_CONTIG_26780_1 2825 2455 2576 chr22 47748585 13073627 13073748 2 45,21,  249,349,  13073627,13073727,