### BAM

# make a section for the new track called tracks.(unique name)
[ tracks.HBR1 ]

# settings for what data is shown in the track
# Symlinked /data/bam to /jbrowse/data/bam
storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = /data/bam/HBR_1.accepted_hits.sorted_by_position.bam
baiUrlTemplate = /data/bam/HBR_1.accepted_hits.sorted_by_position.bam.bai

# settings for how the track looks
category = C Alignments
type = Alignments2
key  = Alignments from sample HBR_1

[ tracks.UHR1 ]

storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = /data/bam/UHR_1.accepted_hits.sorted_by_position.bam
baiUrlTemplate = /data/bam/UHR_1.accepted_hits.sorted_by_position.bam.bai

category = C Alignments
type = Alignments2
key  = Alignments from sample UHR_1

[ tracks.HBR2 ]

# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = /data/bam/HBR_2.accepted_hits.sorted_by_position.bam
baiUrlTemplate = /data/bam/HBR_2.accepted_hits.sorted_by_position.bam.bai

# settings for how the track looks
category = C Alignments
type = Alignments2
key  = Alignments from sample HBR_2

[ tracks.UHR2 ]

# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = /data/bam/UHR_2.accepted_hits.sorted_by_position.bam
baiUrlTemplate = /data/bam/UHR_2.accepted_hits.sorted_by_position.bam.bai

# settings for how the track looks
category = C Alignments
type = Alignments2
key  = Alignments from sample UHR_2

[ tracks.HBR3 ]

storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = /data/bam/HBR_3.accepted_hits.sorted_by_position.bam
baiUrlTemplate = /data/bam/HBR_3.accepted_hits.sorted_by_position.bam.bai

category = C Alignments
type = Alignments2
key  = Alignments from sample HBR_3

[ tracks.UHR3 ]

storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = /data/bam/UHR_3.accepted_hits.sorted_by_position.bam
baiUrlTemplate = /data/bam/UHR_3.accepted_hits.sorted_by_position.bam.bai

category = C Alignments
type = Alignments2
key  = Alignments from sample UHR_3

### BIGWIG files
[ tracks.HBR1_BW ]
key = Genomic coverage plot of HBR1
category = D Genomic coverage
storeClass = JBrowse/Store/SeqFeature/BigWig
type = JBrowse/View/Track/Wiggle/XYPlot
urlTemplate = /data/bigwig/HBR_1.accepted_hits.sorted_by_position.bw
max_score = 100

[ tracks.HBR2_BW ]
key = Genomic coverage plot of HBR2
category = D Genomic coverage
storeClass = JBrowse/Store/SeqFeature/BigWig
type = JBrowse/View/Track/Wiggle/XYPlot
urlTemplate = /data/bigwig/HBR_2.accepted_hits.sorted_by_position.bw
max_score = 100

[ tracks.HBR3_BW ]
key = Genomic coverage plot of HBR3
category = D Genomic coverage
storeClass = JBrowse/Store/SeqFeature/BigWig
type = JBrowse/View/Track/Wiggle/XYPlot
urlTemplate = /data/bigwig/HBR_3.accepted_hits.sorted_by_position.bw
max_score = 100

[ tracks.UHR1_BW ]
key = Genomic coverage plot of UHR1
category = D Genomic coverage
storeClass = JBrowse/Store/SeqFeature/BigWig
type = JBrowse/View/Track/Wiggle/XYPlot
urlTemplate = /data/bigwig/UHR_1.accepted_hits.sorted_by_position.bw
max_score = 100

[ tracks.UHR2_BW ]
key = Genomic coverage plot of UHR2
category = D Genomic coverage
storeClass = JBrowse/Store/SeqFeature/BigWig
type = JBrowse/View/Track/Wiggle/XYPlot
urlTemplate = /data/bigwig/UHR_2.accepted_hits.sorted_by_position.bw
max_score = 100

[ tracks.UHR3_BW ]
key = Genomic coverage plot of UHR3
category = D Genomic coverage
storeClass = JBrowse/Store/SeqFeature/BigWig
type = JBrowse/View/Track/Wiggle/XYPlot
urlTemplate = /data/bigwig/UHR_3.accepted_hits.sorted_by_position.bw
max_score = 100