Custom Track Examples: Difference between revisions

From genomewiki
Jump to navigationJump to search
No edit summary
Line 117: Line 117:
</pre>
</pre>


==Bed Detail=
==Bed Detail==
<pre>
<pre>
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,