Custom Track Examples: Difference between revisions
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==Bed Detail= | ==Bed Detail== | ||
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track name="testDetail4" description="Test detail with bed4" visibility=3 color=175,0,175 type=bedDetail | track name="testDetail4" description="Test detail with bed4" visibility=3 color=175,0,175 type=bedDetail | ||
Revision as of 23:24, 3 November 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://genome-test.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,
Bed Detail
track name="testDetail4" description="Test detail with bed4" visibility=3 color=175,0,175 type=bedDetail chr1 10010044 10023112 NM_013715 NM_013715 9.9999 chr1 10023431 10121982 NM_026493 NM_026493 7.9999 chr1 10122720 10217884 NM_001102430 NM_001102430 8.9999 chr1 10309940 10705157 NM_177834 NM_177834 2.9999 chr1 106596365 106823028 NM_011800 NM_011800 2.9999 chr1 107348686 107491223 NM_013784 NM_013784 5.9999 chr1 107491407 107582678 NM_173187 NM_173187 6.9999 chr1 107608269 107675528 NM_009399 NM_009399 2.9999 chr1 107817952 107861624 NM_001122676 NM_001122676 7.9999 track name="testDetail6" description="Test detail with bed6" visibility=3 color=0,0,255 type=bedDetail chr1 10010044 10023112 NM_013715 9 - NM_013715 9.9999 chr1 10023431 10121982 NM_026493 7 + NM_026493 7.9999 chr1 10122720 10217884 NM_001102430 8 - NM_001102430 8.9999 chr1 10309940 10705157 NM_177834 2 - NM_177834 2.9999 chr1 106596365 106823028 NM_011800 2 + NM_011800 2.9999 chr1 107348686 107491223 NM_013784 5 - NM_013784 5.9999 chr1 107491407 107582678 NM_173187 6 + NM_173187 6.9999 chr1 107608269 107675528 NM_009399 2 + NM_009399 2.9999 chr1 107817952 107861624 NM_001122676 7 + NM_001122676 7.9999 track name="testDetail9" description="Test detail with bed9 and itemRgb" visibility=3 itemRgb=On type=bedDetail chr1 10010044 10023112 NM_013715 9 - 10010192 10023026 243,170,0 NM_013715 9.9999 chr1 10023431 10121982 NM_026493 7 + 10030299 10121359 204,204,36 NM_026493 7.9999 chr1 10122720 10217884 NM_001102430 8 - 10124045 10217708 243,170,0 NM_001102430 8.9999 chr1 10309940 10705157 NM_177834 2 - 10310337 10704941 44,44,208 NM_177834 2.9999 chr1 106596365 106823028 NM_011800 2 + 106761643 106821932 44,44,208 NM_011800 2.9999 chr1 107348686 107491223 NM_013784 5 - 107349550 107485369 97,97,151 NM_013784 5.9999 chr1 107491407 107582678 NM_173187 6 + 107491654 107581170 151,151,94 NM_173187 6.9999 chr1 107608269 107675528 NM_009399 2 + 107608298 107672413 44,44,208 NM_009399 2.9999 chr1 107817952 107861624 NM_001122676 7 + 107818336 107859710 204,204,36 NM_001122676 7.9999 track name="testDetail" description="Test detail with bed12 and itemRgb" visibility=3 itemRgb=On type=bedDetail chr1 10010044 10023112 NM_013715 9 - 10010192 10023026 243,170,0 8 233,149,112,86,66,129,235,229, 0,2272,5768,7508,8427,9177,10098,12839, 1 9.407398424 chr1 10023431 10121982 NM_026493 7 + 10030299 10121359 204,204,36 30 127,109,103,104,81,99,395,87,71,94,58,206,134,79,130,148,153,113,150,147,105,67,118,140,141,47,64,110,139,835, 0,6858,9206,20502,26115,27105,28208,36642,38954,44035,45283,47529,49833,50664,51970,57648,65994,70151,74175,74658,75385,77800,78396,88122,89205,91768,94236,94946,95874,97716, 2 7.300783074 chr1 10122720 10217884 NM_001102430 8 - 10124045 10217708 243,170,0 38 1490,118,139,169,140,133,73,139,136,130,131,161,173,152,170,41,91,151,159,129,152,172,85,206,112,202,109,240,235,134,176,102,277,180,147,157,31,300, 0,2960,4052,5069,7211,9896,14294,15879,16100,16774,19407,20393,22061,22370,23194,23456,26190,35327,35687,36560,42319,43363,46156,46469,46879,51250,51720,51932,56750,61336,62222,67301,71918,75537,76618,78330,79022,94864, 3 8.816714731 chr1 10309940 10705157 NM_177834 2 - 10310337 10704941 44,44,208 11 585,85,203,91,111,105,102,115,125,76,332, 0,4746,12540,83542,84530,152298,156287,159222,164098,270893,394885, 4 2.863425815 chr1 106596365 106823028 NM_011800 2 + 106761643 106821932 44,44,208 12 80,386,295,120,168,188,254,137,122,118,252,1602, 0,165138,172213,173279,176373,178505,185010,202002,206175,210161,215852,225061, 5 2.467133925 chr1 107348686 107491223 NM_013784 5 - 107349550 107485369 97,97,151 31 988,53,43,74,76,56,87,103,103,109,109,92,93,100,140,183,79,56,93,60,41,117,131,125,107,99,122,249,120,74,177, 0,25524,27925,31232,32924,33304,36323,36848,45008,58782,63849,66840,67909,68086,70482,76528,77909,116370,117043,119525,123339,125558,126969,128143,131964,134794,135526,136462,137747,138153,142360, 6 5.258814588 chr1 107491407 107582678 NM_173187 6 + 107491654 107581170 151,151,94 29 773,90,72,56,114,204,92,294,76,96,113,91,72,141,165,148,157,124,49,80,107,100,83,64,139,117,89,71,1629, 0,14302,23088,23269,23421,28045,28351,29023,31567,32640,40070,49988,52917,54914,55591,57407,61788,62482,64079,67340,70657,72062,76574,77436,79350,82208,86461,87112,89642, 7 6.106141423 chr1 107608269 107675528 NM_009399 2 + 107608298 107672413 44,44,208 10 107,82,126,144,94,95,114,53,745,3462, 0,27420,28607,32928,36946,39147,40755,44277,46268,63797, 8 2.461807058 chr1 107817952 107861624 NM_001122676 7 + 107818336 107859710 204,204,36 14 1302,112,77,72,113,95,84,58,133,65,95,129,1482,1982, 0,10525,13694,15609,21296,25593,27813,29442,31320,32794,33258,36997,39346,41690, 9 7.709892986
All Examples
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 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 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 ##Example 6 from Custom Annotation Tracks User's Guide 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,
