hub h1_v4c_hic_DI_v4c
shortLabel h1_v4c_hic_DI_v4c
longLabel Example Hub for useOneFile option
useOneFile on
email yu.xiang@duke.edu

genome hg38

## track loop files
track h1_hicar_5kb
type bigInteract
visibility full
shortLabel h1_hicar_loop
longLabel h1_hicar_loop
#spectrum on
maxHeightPixels 200:100:20
bigDataUrl h1_hicar_5k_sorted.bb
interactUp false
interactMultiRegion padding

track h1_hicar_v4c
type bigInteract
visibility full
shortLabel h1_hicar_v4c_all
longLabel h1_hicar_v4c_all
#spectrum on
maxHeightPixels 200:100:20
bigDataUrl H1_v4c_all.bb
interactUp false
interactMultiRegion padding

track h1_hicar_v4c_recip
type bigInteract
visibility full
shortLabel h1_hicar_v4c_recip
longLabel h1_hicar_v4c_recip
#spectrum on
maxHeightPixels 200:100:20
bigDataUrl H1_v4c_recip.bb
interactUp false
interactMultiRegion padding




## atac track 

track h1_ATAC
type bigWig
bigDataUrl hicar_re1p.final.R2.macs2.bw
viewLimits 0:1
smoothingWindow 2
shortLabel h1_ATAC
longLabel h1_ATAC
visibility full
autoScale off
alwaysZero On
color 0,102,255
maxHeightPixels 100:20:8
windowingFunction maximum


# previouse GM atac track #https://www.encodeproject.org/files/ENCFF603BJO/@@download/ENCFF603BJO.bigWig

## histone marker track 


track h1_H3K27ac-human
type bigWig
smoothingWindow 2
viewLimits 0:15
bigDataUrl https://www.encodeproject.org/files/ENCFF986PCY/@@download/ENCFF986PCY.bigWig
shortLabel h1_H3K27ac
longLabel h1_H3K27ac  
visibility full
autoScale off
alwaysZero On
color 255,153,51
maxHeightPixels 100:20:8
windowingFunction maximum

track h1_H3K27me3-human
type bigWig
smoothingWindow 2
viewLimits 0:15
bigDataUrl https://www.encodeproject.org/files/ENCFF671NVD/@@download/ENCFF671NVD.bigWig
shortLabel h1_H3K27me3
longLabel h1_H3K27me3
visibility full
autoScale off
alwaysZero On
color 153,51,255
maxHeightPixels 100:20:8
windowingFunction maximum





## RNA track for four samples 

track H1_RNA
viewLimits 0:10
bigDataUrl H1_RNA.bigWig
shortLabel H1_RNA
longLabel H1_RNA
type bigWig
color 230,0,0
visibility full
maxHeightPixels 100:20:8
autoScale off
windowingFunction maximum
configurable on

## HiC track 


track h1_hicar_heatmap
type hic
drawMode triangle
shortLabel h1_hicar_heatmap
longLabel h1_hicar_heatmap
color 255,0,0
saturationScore 50
normalization NONE
resolution 10000
autoScale off
visibility full
bigDataUrl h1_5kb.hic

# track h1_hic_heatmap
# type hic
# drawMode triangle
# shortLabel h1_hic_heatmap
# longLabel h1_hic_heatmap
# color 0,0,255
# saturationScore 50
# normalization NONE
# resolution 10000
# autoScale off
# visibility full
# bigDataUrl http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/hic/4DNFIQYQWPF5.hic


# v4c track 
track H1_GATA6_H1_peak_75590
bigDataUrl H1_GATA6_H1_peak_75590.bw
shortLabel H1_GATA6_H1_peak_75590
longLabel H1_GATA6_H1_peak_75590
type bigWig
color 0,153,51
visibility full
maxHeightPixels 100:65:8
autoScale off
viewLimits 0:10
windowingFunction maximum
smoothingWindow 2
configurable on

track H1_DI_score
bigDataUrl H1_peak_DI_score.bw
shortLabel peak_DI_score
longLabel peak_DI_score
type bigWig
color 255,51,153
visibility full
maxHeightPixels 100:20:8
autoScale off
windowingFunction maximum
negateValues on
configurable on


track H1_bin_DI
bigDataUrl Hi_CAR.100kb.direc_index_500000.bw
shortLabel H1_bin_DI
longLabel H1_bin_DI
type bigWig
color 0,0,153
visibility full
maxHeightPixels 100:20:8
autoScale off
windowingFunction maximum
negateValues on
configurable on