Custom Track Examples: Difference between revisions
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Return to CGI testing: http://genomewiki.ucsc.edu/index.php/CGI_Testing | 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. | All examples below can be pasted directly into the custom tracks input menu for hg18. | ||
==RGB Item Example== | ==RGB Item Example== | ||
Revision as of 18:26, 1 September 2010
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 for hg18.
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/examples/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 1000 900 800 700 600 500 400 300 200 100
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,
All Examples
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 track type=bigBed name="bigBed Example" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb browser position chr21:33,031,597-33,041,570 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 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 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 1000 900 800 700 600 500 400 300 200 100 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 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 ##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,
