# Welcome to the UCSC Genome Browser example hub. It includes example stanzas
# for various track types and highlight both the required and commonly
# used settings for these. The example data files below have been trimmed
# to only include data at the default hg38 position, chr7:155,799,529-155,812,871.

# This example hub is designed in a way so that you can modify the settings
# to fit your needs
# To quickly remove the comment (#) lines, after downloading the hub.txt run:
# grep -v ^# hub.txt > hub.no_comments.txt

# This example also uses the "useOneFile on" setting, which allows you to use a
# single file if all of your tracks are on a single genome instead of needing
# separate hub.txt, genomes.txt, and trackDb.txt

#####
# hub config
#####

# This stanza controls overall details for the hub
# a short, unique identifier for your hub, cannot contain any spaces
hub hubBasics
# These label lines control how your hub is labeled in the Genome Browser interface
shortLabel Example Hub
longLabel Example Hub with Basic Settings
# As noted above, this setting allows you place everything in a single file
# You can only use this setting if all your data is on a single genome assembly
useOneFile on
# It is useful to include a contact email in case people have questions about your hub
email genome-www@soe.ucsc.edu

#####
# genome config
#####

# with useOneFile on, you can specify a single genome here
# otherwise if you have multiple genomes, you will need a separate genomes.txt that
# lists all the genomes out & a separate trackDb.txt for each genome
# For details, see: https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup
genome hg38

#####
# bigBed
#####

# This first example is a basic bigBed with the required settings
# the names after the 'track' setting must be unique for every track in this file and cannot contain any spaces
track bigBedRequiredSettings
# label lines control how your tracks are labeled in the interface
shortLabel bigBed Required Settings
longLabel A bigBed Example with Required Settings
# visibility modes include hide/dense/squish/pack/full
# pack is the recommended default display mode for most tracks
visibility pack
# Next, type info - it's composed of 3 parts
# 1: 'bigBed' indicates the basic track type 
# 2: '12' indicates that there are 12 standard bigBed fields
# 3: '+' indicates that there are fields beyond the standard ones
#type bigBed 12 +
type bigBed 5 .
# the url to the bigBed file for this track
# can also be a relative file path for files on the same server
# e.g. bigDataUrl dataFiles/gtexCaviar.bb
bigDataUrl phastConsElem470way.over650_chr7_155799529-155812871.bb
# points to an html description page for that track
html ../templatePage.html
# The priority setting isn't "required", but we're using it to ensure this track shows up at the top
# they must be an integer and lower numbers will be displayed first
priority 1

# This bigBed includes an example of commonly used settings
# The first 6 lines are the same as the previous stanza
track bigBedCommonSettings
shortLabel bigBed Common Settings
longLabel A bigBed Example with Commonly Used Settings
visibility pack
type bigBed 12 +
bigDataUrl gtexCaviar.chr7_155799529-155812871.bb
html ../templatePage.html
priority 10
# Next some commonly used settings
# First, filters
# Filter settings come in pairs, first a label and then the filter itself
# Be sure to place the field name from the bigBed (cpp in this case) after the filter setting
filterLabel.cpp CPP (Causal Posterior Probability)
# We have to give the filter a default value, in this case we've entered 0 as
# we don't want any items filtered out by default
# values in that field range from 0 to 1.0, so you could try 0.5 as a default filter value to remove lower scoring items
filter.cpp 0
# This is similar to the last pair of filter settings, except that we're now filtering
# on the text that's in the "geneName" column
filterLabel.geneName Gene Symbol
# The "*" indicates again that we don't want any items filtered out by default
filterText.geneName *
# Next we have the mouseOver setting, which allows you to control what is
# displayed when someone hovers their cursor over an item in your track
# In this example, first it will display the contents of the name field, then
# a semicolon, and then the text 'CPP:' followed by the contents of the cpp field
mouseOver $name; CPP: $cpp
# You can refer to any field in your file by putting a $ symbol before the field name; Field names come from your .as file 
# These next two settings are useful when your track contains many millions of items
# They have been commented out by default, uncomment them and reload the hub to see how they change the track
# maxItems controls how many items will be displayed on screen before the track switches to a density coverage mode 
#maxItems 100
# maxWindowCoverage does something similar, except it controls the switch to density coverage mode based on bases in the current window
#maxWindowCoverage 10000000
# These next settings are useful for controlling the display of your track, but may not be that crucial for many users
# By default bed tracks with 5+ columns automatically get a filter on that fifth column; it is assumed that this is a "score"
# This setting disables this old-style filter; using any of the new filter settings as described above will also disable the old style filter
#noScoreFilter on
# A list of fields from your bigBed that can be used as the label (e.g. geneName, geneSymbol, etc)
#labelFields name,geneName,geneId,eqtlName

#####
# bigWig
#####

# Next, an example bigWig track
# These first few settings are required for any track, but should be customized to be descriptive
track bigWigExample
shortLabel bigWig Example
longLabel A bigWig Example with Commonly Used Settings
visibility pack
# Next type info - it's composed of two parts
# 1: 'bigWig' indicates the basic track type
# 2: '-20 10.003' indicates the expected data range, i.e. the minimum and maximum values in the bigWig; 
# this range can be quickly determined using our command-line utility bigWigInfo 
type bigWig -20 10.003
bigDataUrl hg38.phyloP100way.chr7_155799529-155812871.bw
# This example uses data that has both positive and negative values
# with just a "color" line, negative values will be colored a lighter shade of the defined color
color 60,60,140
# You can use altColor to color the negative values a different color
#altColor 140,60,60
# autoScale will automatically scale the min/max view limits to the data visible on screen
#autoScale on
# viewLimits allows you to set a static min/max for visible data; if there is data outside that range, you will see pink for those points
#viewLimits -10 10
html ../templatePage.html
priority 15 

#####
# Composite
#####

# Composite tracks allow you to group tracks of the same track type
# For example, if you have several bigWig signal tracks from a set of RNA-seq runs
track compositeExample
shortLabel Example Composite Track
longLabel Example composite track using bigWigs
# This controls the max default visibility for subtracks in the composite
visibility dense
# Composites must have a type declared
type bigWig
priority 2
# "compositeTrack on" indicates that this stanza is for a composite track
compositeTrack on
html ../templatePage.html
priority 20

    # Stanzas for composite subtracks are the same as a normal track
    # except they *must* include a "parent" line
    # they don't need to be indented, but it's often done to make the
    # relationship between the tracks easier to visually discern
    track compositeBigWig1
    bigDataUrl a.chr7_155799529-155812871.bw
    shortLabel bigWig #1
    longLabel bigWig in Composite Track Example #1
    # The "parent" line indicates which composite this track belongs to
    # the value after parent is the 'track' value for the parent track
    parent compositeExample
    type bigWig 0 1
    color 255,0,0
    autoScale group
    visibility dense

    # This stanza is the same as above, except with a different color line
    track compositeBigWig2
    bigDataUrl c.chr7_155799529-155812871.bw
    shortLabel bigWig #2
    longLabel bigWig in Composite Track Example #2
    parent compositeExample
    type bigWig 0 1
    color 0,255,0
    autoScale group
    visibility dense

#####
# Super track
#####

# Super tracks are a more general type container for tracks
# They can contain tracks of different types (e.g. bigWig and bigBed) and even composites
# For example, you might use them to organize all the data resulting from a set of RNA-seq experiments,r
# including signal, peaks, and reads 
# This example contains a bigBed track, a bigWig track, and two composites,
# one containing two bigWigs and the other two bigBeds
track superTrackExample
shortLabel Super Track Example
longLabel A super-track of related data of various types together: individual, multiWig, and composite
# "superTrack on" indicates that this stanza is for a super track
# while the "show" makes the super track visible in the genome browser by default rather than hidden
superTrack on show
html ../templatePage.html
priority 25

    track superTrackbigWig
    parent superTrackExample
    bigDataUrl hg38.phyloP100way.chr7_155799529-155812871.bw
    shortLabel ST bigWig example
    longLabel A super-track-contained bigWig track
    type bigWig -20 10.003
    visibility full
    maxHeightPixels 500:15:8
    viewLimits 1:10
    # The priority setting is used to control the order of tracks in the display
    # Lower numbers will appear earlier in the order
    html ../templatePage.html
    priority 10

    # need an example bigBed here that's no too tall, same for composite below
    track superTrackbigBed
    parent superTrackExample
    bigDataUrl gtexCaviar.chr7_155799529-155812871.bb
    shortLabel ST bigBed example
    longLabel A super-track-contained bigBed
    type bigBed 12 +
    visibility squish
    html ../templatePage.html
    priority 30

    # A composite track stanza in a super track is the same as a normal composite track with the addition of a "parent" line
    track superTrackCompositeBigWig
    parent superTrackExample
    compositeTrack on
    shortLabel ST Composite bigWig
    longLabel A composite track in a super track grouping bigWigs
    visibility dense
    type bigWig
    html ../templatePage.html
    priority 60

        track superTrackCompositeBigWig1
        bigDataUrl a.chr7_155799529-155812871.bw
        shortLabel ST bigWig composite #1
        longLabel A composite-contained bigWig in a super track example #1
        parent superTrackCompositeBigWig on
        type bigWig 0 1

        track superTrackCompositeBigWig2
        bigDataUrl c.chr7_155799529-155812871.bw
        shortLabel ST bigWig composite #2
        longLabel A composite-contained bigWig in a super track example #2
        parent superTrackCompositeBigWig on
        type bigWig 0 1

    track superTrackCompositeBigBed
    parent superTrackExample
    compositeTrack on
    shortLabel ST Composite bigBed
    longLabel A composite track in a super track grouping bigBeds
    visibility dense
    type bigBed
    html ../templatePage.html
    priority 61

        track superTrackCompositeBigBed1
        bigDataUrl phastConsElem470way.over650_chr7_155799529-155812871.bb
        shortLabel ST bigBed composite #1
        longLabel A composite-contained bigBed in a super track example #1
        parent superTrackCompositeBigBed on
        type bigBed 5 .

        track superTrackCompositeBigBed2
        bigDataUrl phastConsElem470way.600-650_chr7_155799529-155812871.bb
        shortLabel ST bigBed composite #2
        longLabel A composite-contained bigBed in a super track example #2
        parent superTrackCompositeBigBed on
        type bigBed 5 .