track gene_phase
type bigBed 9
itemRgb on
shortLabel Gene phase
longLabel Gene phase and amplitude mapped in RGB space (red: 0h, yellow: 6h, green: 12h, blue: 18h)
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/phase_amp/gene_phase_amp.bb
visibility pack
priority 0

track gene_kalman_smoothing_phase_forward
type bigBed 9
itemRgb on
shortLabel Gene kalman smoothing phase forward
longLabel Gene phase by kalman filter forward strand mapped in RGB space (red: 0h, yellow: 6h, green: 12h, blue: 18h)
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/phase_amp/gene_kalman_phase_R2_forward_1000bp.bb
visibility dense
priority 1

track gene_kalman_smoothing_phase_reverse
type bigBed 9
itemRgb on
shortLabel Gene kalman smoothing phase reverse
longLabel Gene phase by kalman filter reverse strand mapped in RGB space (red: 0h, yellow: 6h, green: 12h, blue: 18h)
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/phase_amp/gene_kalman_phase_R2_reverse_1000bp.bb
visibility dense
priority 2

track bin_phase_1000_forward
type bigBed 9
itemRgb on
shortLabel Bin phase forward 1000bp
longLabel forward bin 1000bp phase and amplitude mapped in RGB space (red: 0h, yellow: 6h, green: 12h, blue: 18h)
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/phase_amp/bin_phase_amp_forward_1000bp.bb
visibility dense
priority 3

track bin_phase_1000_reverse
type bigBed 9
itemRgb on
shortLabel Bin phase reverse 1000bp
longLabel reverse bin 1000bp phase and amplitude mapped in RGB space (red: 0h, yellow: 6h, green: 12h, blue: 18h)
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/phase_amp/bin_phase_amp_reverse_1000bp.bb
visibility dense
priority 4

track expressed_regions_1000
type bigBed 3
shortLabel Expressed regions 1000bp
longLabel bin 1000bp Expressed regions
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/expressed_regions_bin1000bp.bb
visibility dense
priority 5

track kalman_expressed_regions_phase_amp_forward_1000
type bigBed 9
itemRgb on
shortLabel Kalman expressed regions phi amp forward 1000bp
longLabel Extended Kalman smoothing phase and amplitude on expressed regions forward strand 1000bp
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/kalman/extended_kalman_on_expressed_regions_forward_bin1000bp_phi_amp.bb
visibility dense
priority 6

track kalman_expressed_regions_phase_amp_reverse_1000
type bigBed 9
itemRgb on
shortLabel Kalman expressed regions phi amp reverse 1000bp
longLabel Extended Kalman smoothing phase and amplitude on expressed regions reverse strand 1000bp
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/kalman/extended_kalman_on_expressed_regions_reverse_bin1000bp_phi_amp.bb
visibility dense
priority 7

track kalman_expressed_regions_ll_forward_1000
type bigWig
itemRgb on
shortLabel Kalman expressed regions ll forward 1000bp
longLabel Extended Kalman smoothing on expressed regions forward strand 1000bp
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/kalman/extended_kalman_on_expressed_regions_forward_bin1000bp_ll.bw
visibility dense
	color 0,0,255
autoScale on
	minLimit 0
maxHeightPixels 100:30:8
priority 8

track kalman_expressed_regions_ll_reverse_1000
type bigWig
itemRgb on
shortLabel Kalman expressed regions ll reverse 1000bp
longLabel Extended Kalman smoothing on expressed regions reverse strand 1000bp
bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/kalman/extended_kalman_on_expressed_regions_reverse_bin1000bp_ll.bw
visibility dense
	color 255,0,0
autoScale on
	minLimit 0
maxHeightPixels 100:30:8
priority 9

track PROseq_forward_1000bp
compositeTrack on
subGroup1 t Time CT00=00 CT04=04 CT08=08 CT12=12 CT16=16 CT20=20 CT28=28 CT24=24 CT32=32 CT36=36 CT40=40 CT44=44
dimensions dimX=t
sortOrder t=+
shortLabel PROseq forward 1000bp
longLabel PRO-seq data composite track forward 1000bp (sum normed count per bin + 1, 1bp: norm count)
type bigWig
visibility full
maxHeightPixels 100:30:8
autoScale group
descriptionUrl PROseq.html
priority 10

	track CT00_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT00
	shortLabel CT00
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT00/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT00_forward.html

	track CT04_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT04
	shortLabel CT04
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT04/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT04_forward.html

	track CT08_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT08
	shortLabel CT08
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT08/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT08_forward.html

	track CT12_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT12
	shortLabel CT12
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT12/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT12_forward.html

	track CT16_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT16
	shortLabel CT16
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT16/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT16_forward.html

	track CT20_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT20
	shortLabel CT20
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT20/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT20_forward.html

	track CT24_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT24
	shortLabel CT24
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT24/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT24_forward.html

	track CT28_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT28
	shortLabel CT28
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT28/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT28_forward.html

	track CT32_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT32
	shortLabel CT32
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT32/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT32_forward.html

	track CT36_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT36
	shortLabel CT36
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT36/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT36_forward.html

	track CT40_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT40
	shortLabel CT40
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT40/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT40_forward.html

	track CT44_forward_1000
	parent PROseq_forward_1000bp on
	subGroups t=CT44
	shortLabel CT44
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT44/NormCoverage_3p_forward_bin1000bp.bw
	type bigWig
	color 0,0,255
	negateValues off
	minLimit 0
	descriptionUrl mm10/CT44_forward.html

track PROseq_reverse_1000bp
compositeTrack on
subGroup1 t Time CT00=00 CT04=04 CT08=08 CT12=12 CT16=16 CT20=20 CT28=28 CT24=24 CT32=32 CT36=36 CT40=40 CT44=44
dimensions dimX=t
sortOrder t=+
shortLabel PROseq reverse 1000bp
longLabel PRO-seq data composite track reverse 1000bp (sum normed count per bin + 1, 1bp: norm count)
type bigWig
visibility full
maxHeightPixels 100:30:8
autoScale group
descriptionUrl PROseq.html
priority 11

	track CT00_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT00
	shortLabel CT00
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT00/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT00_reverse.html

	track CT04_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT04
	shortLabel CT04
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT04/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT04_reverse.html

	track CT08_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT08
	shortLabel CT08
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT08/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT08_reverse.html

	track CT12_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT12
	shortLabel CT12
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT12/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT12_reverse.html

	track CT16_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT16
	shortLabel CT16
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT16/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT16_reverse.html

	track CT20_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT20
	shortLabel CT20
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT20/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT20_reverse.html

	track CT24_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT24
	shortLabel CT24
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT24/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT24_reverse.html

	track CT28_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT28
	shortLabel CT28
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT28/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT28_reverse.html

	track CT32_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT32
	shortLabel CT32
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT32/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT32_reverse.html

	track CT36_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT36
	shortLabel CT36
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT36/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT36_reverse.html

	track CT40_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT40
	shortLabel CT40
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT40/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT40_reverse.html

	track CT44_reverse_1000
	parent PROseq_reverse_1000bp on
	subGroups t=CT44
	shortLabel CT44
	longLabel 
	bigDataUrl https://sv-open.epfl.ch/upnae-public/sites/PROseq/results/GRCm38/binned_norm_coverage/CT44/NormCoverage_3p_reverse_bin1000bp.bw
	type bigWig
	color 255,0,0
	negateValues on
	maxLimit 0
	descriptionUrl mm10/CT44_reverse.html