browser position chr21:33031596-33041570
track db='hg38' name='1 bed3' priority='10' description='CT testing type = bed 3' visibility=pack
chr21	33031596	33034920
chr21	33034920	33038244
chr21	33038244	33041570
track db='hg38' name='2 bed4' priority='20' description='CT testing type = bed 4' visibility=pack
chr21	33031596	33034089	item_0
chr21	33034089	33036582	item_1
chr21	33036582	33039075	item_2
chr21	33039075	33041570	item_3
track db='hg38' name='3 bed5' priority='30' description='CT testing type = bed 5' visibility=pack
chr21	33031596	33033590	item_0	0
chr21	33033590	33035584	item_1	100
chr21	33035584	33037578	item_2	200
chr21	33037578	33039572	item_3	300
chr21	33039572	33041570	item_4	400
track db='hg38' name='4 bed6' priority='40' description='CT testing type = bed 6' visibility=pack
chr21	33031596	33033258	item_0	0	-
chr21	33033258	33034920	item_1	100	+
chr21	33034920	33036582	item_2	200	-
chr21	33036582	33038244	item_3	300	+
chr21	33038244	33039906	item_4	400	-
chr21	33039906	33041570	item_5	500	+
track db='hg38' name='5 bed8' priority='50' description='CT testing type = bed 8' visibility=pack
chr21	33031596	33032842	item_0	0	-	33031658	33032780
chr21	33032842	33034088	item_1	100	+	33032945	33033985
chr21	33034088	33035334	item_2	200	-	33034150	33035272
chr21	33035334	33036580	item_3	300	+	33035437	33036477
chr21	33036580	33037826	item_4	400	-	33036642	33037764
chr21	33037826	33039072	item_5	500	+	33037929	33038969
chr21	33039072	33040318	item_6	600	-	33039134	33040256
chr21	33040318	33041570	item_7	700	+	33040422	33041466
track db='hg38' name='6 bed9' priority='60' description='CT testing type = bed 9' visibility=pack itemRgb='On'
chr21	33031596	33032704	item_0	0	-	33031651	33032649	255,0,0
chr21	33032704	33033812	item_1	100	+	33032796	33033720	238,68,0
chr21	33033812	33034920	item_2	200	-	33033867	33034865	204,102,0
chr21	33034920	33036028	item_3	300	+	33035012	33035936	170,136,0
chr21	33036028	33037136	item_4	400	-	33036083	33037081	136,170,0
chr21	33037136	33038244	item_5	500	+	33037228	33038152	96,192,32
chr21	33038244	33039352	item_6	600	-	33038299	33039297	68,238,0
chr21	33039352	33040460	item_7	700	+	33039444	33040368	0,255,0
chr21	33040460	33041570	item_8	800	-	33040515	33041515	255,0,0
track db='hg38' name='7 bed12' priority='70' description='CT testing type = bed 12' visibility=pack itemRgb='On'
chr21	33031596	33032427	item_0	0	-	33031637	33032386	255,0,0	3	166,166,166	0,332,665

chr21	33032427	33033258	item_1	100	+	33032496	33033189	238,68,0	2	277,277	0,554

chr21	33033258	33034089	item_2	200	-	33033299	33034048	204,102,0	3	166,166,166	0,332,665

chr21	33034089	33034920	item_3	300	+	33034158	33034851	170,136,0	2	277,277	0,554

chr21	33034920	33035751	item_4	400	-	33034961	33035710	136,170,0	3	166,166,166	0,332,665

chr21	33035751	33036582	item_5	500	+	33035820	33036513	96,192,32	2	277,277	0,554

chr21	33036582	33037413	item_6	600	-	33036623	33037372	68,238,0	3	166,166,166	0,332,665

chr21	33037413	33038244	item_7	700	+	33037482	33038175	0,255,0	2	277,277	0,554

chr21	33038244	33039075	item_8	800	-	33038285	33039034	255,0,0	3	166,166,166	0,332,665

chr21	33039075	33039906	item_9	900	+	33039144	33039837	238,68,0	2	277,277	0,554

chr21	33039906	33040737	item_10	0	-	33039947	33040696	204,102,0	3	166,166,166	0,332,665

chr21	33040737	33041570	item_11	100	+	33040806	33041501	170,136,0	2	277,277	0,556

track type=wiggle_0 priority='80' name='8 Wiggle bedGraph Format' description='wiggle bedGraph format thru zero' visibility=full color=200,100,0 altColor=0,100,200
chr21	33031597	33032705	 -1.00
chr21	33032705	33033813	 -0.75
chr21	33033813	33034921	 -0.50
chr21	33034921	33036029	 -0.25
chr21	33036029	33037137	  0.00
chr21	33037137	33038245	  0.25
chr21	33038245	33039353	  0.50
chr21	33039353	33040461	  0.75
chr21	33040461	33041569	  1.00
track type=wiggle_0 priority='90' name='9 Wiggle bedGraph to zero' description='wiggle bedGraph format to zero' visibility=full color=200,100,0 altColor=0,100,200
chr21	33031597	33032705	 -1.00
chr21	33032705	33033813	 -0.75
chr21	33033813	33034921	 -0.50
chr21	33034921	33036029	 -0.25
chr21	33036029	33037137	  0.00
chr21	33037137	33038245	 -0.25
chr21	33038245	33039353	 -0.50
chr21	33039353	33040461	 -0.75
chr21	33040461	33041569	 -1.00
track type=wiggle_0 priority='100' name='10 Wiggle bedGraph from zero' description='wiggle bedGraph format from zero' visibility=full color=200,100,0 altColor=0,100,200
chr21	33031597	33032705	  1.00
chr21	33032705	33033813	  0.75
chr21	33033813	33034921	  0.50
chr21	33034921	33036029	  0.25
chr21	33036029	33037137	  0.00
chr21	33037137	33038245	  0.25
chr21	33038245	33039353	  0.50
chr21	33039353	33040461	  0.75
chr21	33040461	33041569	  1.00
track type=wiggle_0 priority='110' name='11 wiggle variableStep' description='variableStep format' visibility=full autoScale=off viewLimits=5.0:25.0 color=255,200,0 yLineMark=11.76 yLineOnOff=on
variableStep chrom=chr21 span=1108
33031597	10.0
33032705	12.5
33033813	15.0
33034921	17.5
33036029	20.0
33037137	17.5
33038245	15.0
33039353	12.5
33040461	10.0
track type=wiggle_0 priority='120' name='12 wiggle fixedStep' description='wiggle fixed step graphType=points' visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 graphType=points
fixedStep chrom=chr21 start=33031597 step=1108 span=997
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track type=bigWig priority='80' name='13 bigWig bedGraph thru 0' description='bigWig from bedGraph format thru zero' visibility=full color=200,100,0 altColor=0,100,200 bigDataUrl="http://hgwdev.gi.ucsc.edu/~hiram/ctDb/wigBedGraphThruZero.bw"
track type=bigWig priority='90' name='14 bigWig bedGraph to zero' description='bigWig from bedGraph format to zero' visibility=full color=200,100,0 altColor=0,100,200 bigDataUrl="http://hgwdev.gi.ucsc.edu/~hiram/ctDb/wigBedGraphToZero.bw"
track type=bigWig priority='100' name='15 bigWig bedGraph from zero' description='bigWig from bedGraph format from zero' visibility=full color=200,100,0 altColor=0,100,200 bigDataUrl="http://hgwdev.gi.ucsc.edu/~hiram/ctDb/wigBedGraphFromZero.bw"
track type=bigWig priority='110' name='16 bigWig variableStep' description='bigWig variableStep format' visibility=full autoScale=off viewLimits=5.0:25.0 color=255,200,0 yLineMark=11.76 yLineOnOff=on bigDataUrl="http://hgwdev.gi.ucsc.edu/~hiram/ctDb/wigVariableStep.bw"
track type=bigWig priority='120' name='17 bigWig fixedStep' description='bigWig fixed step graphType=points' visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 graphType=points bigDataUrl="http://hgwdev.gi.ucsc.edu/~hiram/ctDb/wigFixedStep.bw"
track type=bigWig priority='120' name='18 bigWig fixedStep log' description='bigWig fixed step graphType=points log scale' transformFunc=log visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 graphType=points bigDataUrl="http://hgwdev.gi.ucsc.edu/~hiram/ctDb/wigFixedStep.bw"
track type=bam priority='140' name='19 BAM Example One' description='Bam Ex. 1: 1000 Genomes read alignments (individual NA12878)' pairEndsByName=. pairSearchRange=10000 chromosomes=chr21 bamColorMode=gray maxWindowToDraw=200000 db=hg38 visibility=squish bigDataUrl=http://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bamExample.bam
track type=bigBed db='hg38' name='20 bigBed3' priority='150' description='CT testing type = bigBed 3' bigDataUrl='http://hgwdev.gi.ucsc.edu/~hiram/ctDb/bigBedType03.bb' visibility=pack
track type=bigBed db='hg38' name='21 bigBed4' priority='160' description='CT testing type = bigBed 4' bigDataUrl='http://hgwdev.gi.ucsc.edu/~hiram/ctDb/bigBedType04.bb' visibility=pack
track type=bigBed db='hg38' name='22 bigBed5' priority='170' description='CT testing type = bigBed 5' bigDataUrl='http://hgwdev.gi.ucsc.edu/~hiram/ctDb/bigBedType05.bb' visibility=pack
track type=bigBed db='hg38' name='23 bigBed6' priority='180' description='CT testing type = bigBed 6' bigDataUrl='http://hgwdev.gi.ucsc.edu/~hiram/ctDb/bigBedType06.bb' visibility=pack
track type=bigBed db='hg38' name='24 bigBed8' priority='190' description='CT testing type = bigBed 8' bigDataUrl='http://hgwdev.gi.ucsc.edu/~hiram/ctDb/bigBedType08.bb' visibility=pack
track type=bigBed db='hg38' name='25 bigBed9' priority='200' description='CT testing type = bigBed 9' bigDataUrl='http://hgwdev.gi.ucsc.edu/~hiram/ctDb/bigBedType09.bb' visibility=pack itemRgb='On'
track type=bigBed db='hg38' name='26 bigBed12' priority='210' description='CT testing type = bigBed 12' bigDataUrl='http://hgwdev.gi.ucsc.edu/~hiram/ctDb/bigBedType12.bb' visibility=pack itemRgb='On'
track name=GFF example description="GFF TeleGene(tm) Regulatory Regions" visibility=2
chr21	TeleGene	enhancer	33031596	33200100	500	+	.	touch1
chr21	TeleGene	promoter	33037136	33210100	900	+	.	touch2
chr21	TeleGene	promoter	33039136	33225000	800	-	.	touch3
track name=GTF example description="GTF table browser output UCSC Genes"
chr21	hg19_knownGene	exon	33026871	33027740	0.000000	-	.	gene_id "uc002yoz.1"; transcript_id "uc002yoz.1"; 
chr21	hg19_knownGene	exon	33030247	33030540	0.000000	-	.	gene_id "uc002yoz.1"; transcript_id "uc002yoz.1"; 
chr21	hg19_knownGene	exon	33031710	33031813	0.000000	-	.	gene_id "uc002yoz.1"; transcript_id "uc002yoz.1"; 
chr21	hg19_knownGene	start_codon	33032083	33032085	0.000000	+	.	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	CDS	33032083	33032154	0.000000	+	0	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	exon	33031935	33032154	0.000000	+	.	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	CDS	33036103	33036199	0.000000	+	0	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	exon	33036103	33036199	0.000000	+	.	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	CDS	33038762	33038831	0.000000	+	2	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	exon	33038762	33038831	0.000000	+	.	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	CDS	33039571	33039688	0.000000	+	1	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	exon	33039571	33039688	0.000000	+	.	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	CDS	33040784	33040888	0.000000	+	0	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	stop_codon	33040889	33040891	0.000000	+	.	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
chr21	hg19_knownGene	exon	33040784	33041243	0.000000	+	.	gene_id "uc002ypa.3"; transcript_id "uc002ypa.3"; 
track type=pgSnp visibility=3 db=hg38 name="pgSnp" description="Personal Genome SNP example"
browser position chr21:33031924-33032937
chr21   33032007 33032008       T/G     2       21,70   90,70
chr21   33032031 33032032       T/G/A   3       9,60,7  80,80,30
chr21   33032035 33032035       -/CGG   2       20,80   0,0
chr21   33032088 33032093       -/CTCGG 2       30,70   0,0
chr21   33032277 33032278       T       1       15      90
chr21   33032771 33032772       A       1       36      80
chr21   33032827 33032828       A/T     2       15,5    0,0
chr21   33032879 33032880       C       1       0       0
chr21   33032915 33032916       -       1       0       0
track type=vcfTabix name="VCF Example One" description="VCF Ex. 1: 1000 Genomes phase 1 interim SNVs" chromosomes=chr21 maxWindowToDraw=200000 db=hg38 visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/vcfExample.vcf.gz
track type=broadPeak visibility=pack db=hg38 name="bPk" description="ENCODE broadPeak Example"
chr21     33031596       33034089 .       116      .       4.89716 3.70716 -1
chr21     33034089       33036582 .       503      .       2.46426 1.54117 -1
chr21     33036582       33039075 .       907      .       3.22803 2.12614 -1
track type=narrowPeak visibility=pack db=hg38 name="nPk" description="ENCODE narrowPeak Example"
chr21    33033812 33034920 .       100       .       182     5.0945  -1  50
chr21    33036028 33037136 .       400       .       910      4.6052  -1  40
chr21    33039352 33040460 .       900       .       482     9.2103  -1  75
track name="Blat PSL" description="PSL example BLAT search output" visibility=full
9975  0          0    0                0       0    0      0       +    YourSeq 9975    0       9975    chr21   48129895 33031595 33041570 1 9975, 0, 33031595,
track name=testBedDetail type=bedDetail description="Test bedDetail set from Rachel" visibility=3
chr2	74803744	74808800	intron22	0	-	intron22	BC025997.1
chr2	170460203	170460535	intron20	0	+	intron20	BC063711.1,BC073875.1
chr2	170462655	170463613	intron21	0	+	intron21	BC063711.1,BC073875.1
chr2	170463657	170465180	intron26	0	+	intron26	BC063711.1,BC073875.1
chr2	170488442	170489669	intron27	0	+	intron27	BC073875.1
chr2	170460770	170462548	intron24	0	+	intron24	BC063711.1,BC073875.1
chr2	74786835	74787277	intron25	0	-	intron25	BC025997.1
chr2	74802705	74803582	intron41	0	-	intron41	BC025997.1
chr2	170441408	170460151	intron42	0	+	intron42	BC063711.1
chr2	74867453	74875099	intron9	0	-	intron9	BC025997.1
chr2	170460611	170460696	intron8	0	+	intron8	BC063711.1,BC073875.1
chr2	74786000	74786824	intron36	0	-	intron36	BC025997.1
chr2	170465267	170470973	intron31	0	+	intron31	BC063711.1,BC073875.1
chr2	74834349	74842090	intron30	0	-	intron30	BC025997.1
chr21	32986708	33086457	testExample1	0	+	testExample1	BC093007.1,AF100757.1,AK223178.1,BC009292.2,BC004302.1
chr21	33035835	33036709	testExample2	0	+	testExample2	BC093007.1,AF100757.1,AK223178.1,BC009292.2,BC004302.1
chr21	33006708	33086457	testExample3	0	+	testExample3	BC093007.1,AF100757.1,AK223178.1,BC009292.2,BC004302.1
track type=bigGenePred baseColorDefault=genomicCodons visibility=full name="bigGenePred" description="A bigGenePred file with sparse hg19 data" bigDataUrl=https://genecats.gi.ucsc.edu/qa/customTracks/testing/hg19bigGenePred.bb
track type="longTabix" name="longRange" bigDataUrl=http://hgwdev.cse.ucsc.edu/~braney/longRange/Esc_40kb_hindIII_rep1.over10.gz
track type=bigChain name="bigChain Example One" description="A bigChain file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigChain.bb linkDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigChain.link.bb
track type=bigPsl name="bigPsl Example One" description="A bigPsl file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigPsl.bb
track type=bam visibility=full doWiggle=on name=exampleCRAM bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/cramExample.cram
track type=interact name="interact Example Text" description="An interact file text" interactDirectional=true maxHeightPixels=200:100:50 visibility=full interactUp=true
chr21	33030690	33036618	ENSG00000238390/GH21J031658	12	25.5	eQTLs,C-HiC,Distance	126,47,142	chr21	33030690	33033576	GH21J031658	.	chr21	33036617	33036618	ENSG00000238390	+
chr21	33030690	33033576	SOD1/GH21J031658	554	1360.43	eRNA_co-expression,Distance	237,177,32	chr21	33030690	33033576	GH21J031658	.	chr21	33031933	33031934	SOD1	+
track type=bigInteract visibility=full name="interact bb Example" description="A bigInteract file" useScore=true bigDataUrl=https://genecats.gi.ucsc.edu/qa/customTracks/testing/hg19interact.bb
track type=hic name="hic Example ONE" description="hic Ex. 1: in situ Hi-C on HMEC" db=hg38 visibility=dense color=0,0,0 drawMode=arc saturationScore=12 normalization=KR resolution=5000 bigDataUrl=https://hgdownload2.gi.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_HMEC_combined.hic
browser position chr21:32,000,000-35,000,000
track type=hic name="hic Example TWO" description="hic Ex. 2: in situ Hi-C on HMEC" db=hg38 visibility=dense color=0,255,0 drawMode=square saturationScore=50 normalization=VC_SQRT resolution=10000 bigDataUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_HMEC_combined.hic
#browser position chr21:32,000,000-35,000,000
