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<!-- This file contains custom track documentation included in -->
<!-- hgTracksHelp.html and customTrack.html. -->
<p>
The Genome Browser provides dozens of aligned annotation tracks that have been computed at UCSC or
have been provided by outside collaborators. In addition to these standard tracks, it is also
possible for users to upload their own annotation data for temporary display in the browser. These
custom annotation tracks are viewable only on the machine from which they were uploaded and are
automatically discarded 48 hours after the last time they are accessed, unless they are saved in a
<a href="/goldenPath/help/hgSessionHelp.html#CTs">Session</a>. Optionally, users can make custom
annotations viewable by others as well. For a more stable option for custom annotations, we suggest
using <a href="hgTrackHubHelp.html" target="_blank">track hubs</a>. A third, more technical, option
is to operate a mirror. Custom tracks work well for quickly displaying data, while track hubs are
more configurable and permanent.</p>
<p>
Custom tracks are a wonderful tool for research scientists using the Genome Browser. Because space
is limited in the Genome Browser track window, many excellent genome-wide tracks cannot be included
in the standard set of tracks packaged with the browser. Other tracks of interest may be excluded
from distribution because the annotation track data is too specific to be of general interest or
can't be shared until journal publication. In the past, many individuals and labs contributed custom
tracks to the Genome Browser website for use by others. To view a list of these custom annotation
tracks, click <a href="../customTracks/custTracks.html">here</a>.</p>
<p>
Track hubs are now the preferred approach for viewing and sharing data on the Browser. Labs,
consortia, and institutions submit their hubs to be listed as a <a href="hgTrackHubHelp.html#View"
target="_blank">Public Hub</a>. Track hubs require remotely hosted data. They use binary index
files which allow the browser to quickly access only what is relevant for the current region being
viewed in the browser. See the <a href="hgTrackHubHelp.html" target="_blank">track hub help
page</a> for more information.</p>
<p>
Genome Browser annotation tracks are based on files in line-oriented format. Each line in the file
defines a display characteristic for the track or defines a data item within the track. Annotation
files contain three types of lines: browser lines, track lines, and data lines. Empty lines and
those starting with "#" are ignored.</p>
<p>
To construct an annotation file and display it in the Genome Browser, follow these steps:</p>
<a name="format"></a>
<p>
<strong>Step 1. </strong> Format the data set: <br>
Format your data as a tab-separated file using one of the formats supported by the Genome
Browser. Annotation data can be in standard
<a href="../../FAQ/FAQformat.html#format3">GFF</a> format or in a format designed specifically for the Human Genome Project or UCSC Genome Browser, including
<a href="bedgraph.html">bedGraph</a>,
<a href="../../FAQ/FAQformat.html#format4">GTF</a>,
<a href="../../FAQ/FAQformat.html#format2">PSL</a>,
<a href="../../FAQ/FAQformat.html#format1">BED</a>,
<a href="bigBed.html">bigBed</a>,
<a href="wiggle.html">WIG</a>,
<a href="bigGenePred.html">bigGenePred</a>,
<a href="bigNarrowPeak.html">bigNarrowPeak</a>,
<a href="bigMaf.html">bigMaf</a>,
<a href="bigChain.html">bigChain</a>,
<a href="bigPsl.html">bigPsl</a>,
<a href="barChart.html">barChart</a>,
<a href="barChart.html">bigBarChart</a>,
<a href="interact.html">interact</a>,
<a href="interact.html">bigInteract</a>,
<a href="bigWig.html">bigWig</a>,
<a href="bam.html">BAM</a>,
<a href="cram.html">CRAM</a>,
<a href="vcf.html">VCF</a>,
<a href="maf.html">MAF</a>,
<a href="../../FAQ/FAQformat.html#format1.7">BED detail</a>,
<a href="../../FAQ/FAQformat.html#format10">Personal Genome SNP</a>,
<a href="../../FAQ/FAQformat.html#format13">broadPeak</a>,
<a href="../../FAQ/FAQformat.html#format12">narrowPeak</a>,
and <a href="../../FAQ/FAQformat.html#format6.5">microarray</a>
(BED15). GFF and GTF files <em>must</em> be tab-delimited rather than space-delimited to display
correctly. Chromosome references must be of the form <em>chrN</em> (the parsing of chromosome names
<em><strong>is</strong></em> case-sensitive). You may include more than one data set in your
annotation file; these need not be in the same format.</p>
<p>
<strong>Step 2.</strong> Define the Genome Browser display characteristics:<br>
Add one or more optional <a href="#lines">browser lines</a> to the beginning of your formatted data
file to configure the overall display of the Genome Browser when it initially shows your annotation
data. Browser lines allow you to configure such things as the genome position that the Genome
Browser will initially open to, the width of the display, and the configuration of the other
annotation tracks that are shown (or hidden) in the initial display. NOTE: If the browser position
is not explicitly set in the annotation file, the initial display will default to the position
setting most recently used by the user, which may not be an appropriate position for viewing the
annotation track.</p>
<p>
<strong>Step 3.</strong> Define the annotation track display characteristics: <br>
Following the browser lines--and immediately preceding the formatted data--add a
<a href="#TRACK">track line</a> to define the display attributes for your annotation data set. Track
lines enable you to define annotation track characteristics such as the name, description, colors,
initial display mode, use score, etc. The track <a href="#TRACK">type=<<em>track_type</em>></a>
attribute is required for some tracks. If you have included more than one data set in your
annotation file, insert a track line at the beginning of each new set of data.</p>
<a name="EXAMPLE1"></a>
<p>
<strong><em>Example #1:</em></strong>
Here is an example of a simple annotation file that contains a list of chromosome coordinates.
<pre><code>browser position chr22:20100000-20100900
track name=coords description="Chromosome coordinates list" visibility=2
#chrom chromStart chromEnd
chr22 20100000 20100100
chr22 20100011 20100200
chr22 20100215 20100400
chr22 20100350 20100500
chr22 20100700 20100800
chr22 20100700 20100900</code></pre>
<p>
Click <a class="insideLink" href="../../cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/examples/ct_example1.txt"
target="_blank">here</a> to view this track in the Genome Browser.</p>
<p>
<strong><em>Example #2:</em></strong>
Here is an example of an annotation file that defines 2 separate annotation tracks in BED format.
The first track displays blue one-base tick marks every 10000 bases on chr22. The second track
displays red 100-base features alternating with blank space in the same region of chr22.
<pre><code>browser position chr22:20100000-20140000
track name=spacer description="Blue ticks every 10000 bases" color=0,0,255,
#chrom chromStart chromEnd
chr22 20100000 20100001
chr22 20110000 20110001
chr22 20120000 20120001
track name=even description="Red ticks every 100 bases, skip 100" color=255,0,0
#chrom chromStart chromEnd name
chr22 20100000 20100100 first
chr22 20100200 20100300 second
chr22 20100400 20100500 third</code></pre>
<p>
Click <a class="insideLink" href="../../cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/examples/ct_example2.txt"
target="_blank">here</a> to view this track in the Genome Browser.</dd</p>
<p>
<strong><em>Example #3a:</em></strong>
This example shows an annotation file containing one data set in BED format. The track displays
features with multiple blocks, a thick end and thin end, and hatch marks indicating the direction of
transcription. The track labels display in green (0,128,0), and the gray level of the each feature
reflects the score value of that line.
<pre><code>browser position chr22:1000-10000
browser hide all
track name="BED track" description="BED format custom track example" visibility=2 color=0,128,0 useScore=1
#chrom chromStart chromEnd name score strand thickStart thickEnd itemRgb blockCount blockSizes blockStarts
chr22 1000 5000 itemA 960 + 1100 4700 0 2 1567,1488, 0,2512
chr22 2000 7000 itemB 200 - 2200 6950 0 4 433,100,550,1500 0,500,2000,3500 </code></pre>
<p>
Click
<a class="insideLink" href="../../cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/examples/ct_example3.txt"
target="_blank">here</a> to view this track in the Genome Browser.</p>
<p>
<strong><em>Example #3b:</em></strong>
This example shows a simple annotation file containing one data set in the bigBed format. This track
displays random sized blocks across chr21 in the human genome. The big data formats, such as the
bigBed format, can be uploaded using a bigDataUrl that is specified in the track line. For more
information on these track line parameters, refer to the <a href="#TRACK">Track Lines</a>
section. When using bigDataUrls, data is cached and updated every 300 seconds. If you are updating
your big data tracks with different displays and are not seeing your track changes in the browser,
you may want to add the <a href="hgTrackHubHelp.html#Debug">udcTimeout</a>= parameter to prevent
caching of your track data and force a reload.</p>
<p>
You may paste these two lines directly into the "Add Custom Tracks" page to view this example in the
browser:</p>
<pre><code>browser position chr21:33,031,597-33,041,570
track type=bigBed name="bigBed Example One" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</code></pre>
<p>
Alternatively, you may also upload just the URL of the bigBed file:</p>
<pre><code>http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb </code></pre>
<p>
This will infer the track type as "bigBed" based on the file extension and set the track
name to "bigBedExample".</p>
<p>
<strong>Step 4. Display your annotation track in the Genome Browser</strong><br>
From the <a href="../../cgi-bin/hgGateway">Gateway page</a>, select the
genome assembly on which your annotation data is based, click 'GO', then click the "add custom
tracks" or "manage custom tracks" button below the tracks window.</p>
<p>
On the Add Custom Tracks page, load the annotation track data or URL for your custom track into the
upper text box and the track documentation (optional) into the lower text box, then click the
"Submit" button. Tracks may be loaded by entering text, a URL, or a pathname on your local computer.
The track <a href="#TRACK">type=<<em>track_type</em>></a> attribute is required for some tracks.
For more information on these methods, as well as information on creating and adding track
documentation, see <a href="#ADD_CT">Loading a Custom Track into the Genome Browser</a>.</p>
<p>
If you encounter difficulties displaying your annotation, read the section
<a href="#TROUBLE">Troubleshooting Annotation Display Problems</a>.</p>
<p><strong>Step 5. (Optional) Add details pages for individual track features</strong><br>
After you've constructed your track and have successfully displayed it in the Genome Browser, you
may wish to customize the details pages for individual track features. The Genome Browser
automatically creates a default details page for each feature in the track containing the feature's
name, position information, and a link to the corresponding DNA sequence. To view the details page
for a feature in your custom annotation track (in full, pack, or squish display mode), click on the
item's label in the annotation track window.</p>
<p>
You can add a link from a details page to an external web page containing additional information
about the feature by using the track line <em>url</em> attribute. In the annotation file, set the
<em>url</em> attribute in the track line to point to a publicly available page on a web server. The
<em>url</em> attribute substitutes each occurrence of '$$' in the URL string with the name defined
by the <em>name</em> attribute. You can take advantage of this feature to provide individualized
information for each feature in your track by creating HTML anchors that correspond to the feature
names in your web page.</p>
<p><strong><em>Example #4:</em></strong>
Here is an example of a file in which the <em>url</em> attribute has been set to point to the file
<a href="cloneshtml.txt" target="_blank">http://genome.ucsc.edu/goldenPath/help/clones.html</a>. The
'#$$' appended to the end of the file name in the example points to the HTML NAME tag within the
file that matches the name of the feature (cloneA, cloneB, etc.).</p>
<pre><code>browser position chr22:10000000-10020000
browser hide all
track name=clones description="Clones" visibility=2 color=0,128,0 useScore=1 url="http://genome.ucsc.edu/goldenPath/help/clones.html#$$"
#chrom chromStart chromEnd name score
chr22 10000000 10004000 cloneA 960
chr22 10002000 10006000 cloneB 200
chr22 10005000 10009000 cloneC 700
chr22 10006000 10010000 cloneD 600
chr22 10011000 10015000 cloneE 300
chr22 10012000 10017000 cloneF 100 </code></pre>
<p>
Click
<a class="insideLink" href="../../cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/examples/ct_example4.txt"
target="_blank">here</a> to display this track in the Genome Browser.</p>
<p>
<strong>Step 6. (Optional) Share your annotation track with others</strong><br>
The previous steps showed you how to upload annotation data for your own use on your own machine.
However, many users would like to share their annotation data with members of their research group
on different machines or with colleagues at other sites. To learn how to make your Genome Browser
annotation track viewable by others, read the section <a href="#SHARE">Sharing Your Annotation Track
with Others</a>.</p>
<a name="ADD_CT"></a>
<h2>Loading a custom track into the Genome Browser</h2>
<p>
Using the Genome Browser's custom track upload and management utility, annotation tracks may be
added for display in the Genome Browser, deleted from the Genome Browser, or updated with new data
and/or display options. You may also use this interface to upload and manage custom track sets for
multiple genome assemblies.</p>
<p>
To load a custom track into the Genome Browser:</p>
<p>
<strong>Step 1. Open the Add Custom Tracks page</strong><br>
Select the top blue bar "My Data" menu and click <a href="../../cgi-bin/hgCustom">Custom
Tracks</a>. Or, when browsing tracks, click the "add custom tracks" button below the
<a href="../../cgi-bin/hgTracks">Genome Browser</a>. (Note: if one or more tracks have already
been uploaded during the current Browser session, additional tracks may be loaded on the Manage
Custom Tracks page. In this case, the button on the Browser page will be labeled "manage
custom tracks" and will automatically direct you to the track management page. See
<a href="#MANAGE_CT">Displaying and Managing Custom Tracks</a> for more information.)</p>
<p>
<strong>Step 2. Load the custom track data</strong><br>
The Add Custom Tracks page contains separate sections for uploading custom track data and optional
custom track descriptive documentation. Load the annotation data into the upper section by one of
the following methods:</p>
<ul>
<li>
Enter one or more URLs for custom tracks (one per line) in the data text box. The Genome Browser
supports both the HTTP and FTP (passive-only) protocols. Data provided by a URL may need to be
proceeded by a separate line defining <a href="#TRACK">type=<<em>track_type</em>></a> required
for some tracks, for example such as "track type=broadPeak".</li>
<li>
Click the "Choose File" button directly above the data text box, then choose a custom track
file from your local computer.
# or type the pathname of the file into the "upload" text
box adjacent to the "Browse" button.
The custom track data may be compressed by any of
the following programs: gzip (<em>.gz</em>), compress (<em>.Z</em>), or bzip2 (<em>.bz2</em>).
Files containing compressed data must include the appropriate suffix in their names.</li>
<li>
Paste or type the custom track data directly into the data box. Because the text in this box will
not be saved to a file, this method is not recommended unless you have a copy of the data
elsewhere.</li>
</ul>
<p>
Multiple custom tracks may be uploaded at one time on the Add Custom Tracks page through one of the
following methods:</p>
<ul>
<li>
Put all the tracks into the same file (rather than separate files), then load the file via the
"Choose File" button.</li>
<li>
Place your track files in a web-accessible location on your server, then load them into the Genome
Browser by pasting their URLs into the text input box.</li>
</ul>
<p>
<strong><em>NOTE: Please limit the number of custom tracks that you upload and maintain to less
than 1000 tracks. If you have more than this suggested limit of 1000 tracks, please consider
setting up a <a href="hgTrackHubHelp.html" target="_blank">track hub</a> instead.</em></strong></p>
<p>
<strong>Step 3. (Optional) Load the custom track description page</strong><br>
If desired, you can provide optional descriptive text (in plain or HTML format) to accompany your
custom track. This text will be displayed when a user clicks the track's description button on the
Genome Browser annotation tracks page. Descriptive text may be loaded by one of the following
methods:</p>
<ul>
<li>
Click the "Choose File" button directly above the documentation text box, then choose a text
file from your local computer.</li>
<li>
Paste or type the custom track data directly into the text input box. Note that the text in this box
will not be saved to a file; therefore, this method is not recommended except for temporary
documentation purposes.</li>
<li>
If your descriptive text is located on a website, you can reference it from your custom track file
by defining the track line attribute "htmlUrl":
<strong>htmlUrl=<<em>external_url</em>></strong>. In this case, there is no need to insert
anything into the documentation text box.</li>
</ul>
<p>
To format your description page in a style that is consistent with standard Genome Browser tracks,
click the template link below the documentation text box for an HTML <a href="ct_description.txt"
target="_blank">template</a> that may be copied and pasted into a file for editing.</p>
<p>
If you load multiple custom tracks simultaneously using one of the methods described in Step 2, a
track description can be associated only with the last custom track loaded, unless you upload the
descriptive text using the track line "htmlUrl" attribute described above.</p>
<p>
<strong>Step 4. Upload the track</strong><br>
Click the <em>Submit</em> button to load your custom track data and documentation into the Genome
Browser. If the track uploads successfully, you will be directed to the custom track management page
where you can display your track, update an uploaded track, add more tracks, or delete uploaded
tracks. If the Genome Browser encounters a problem while loading your track, it will display an
error. See the section <a href="#TROUBLE">Troubleshooting Annotation Display Problems</a> for help
in diagnosing custom track problems.
<p>
<strong><em>NOTE: Please limit the number of custom tracks that you upload and maintain to less
than 1000 tracks. If you have more than this suggested limit of 1000 tracks, please consider
setting up a <a href="hgTrackHubHelp.html" target="_blank">track hub</a> instead.</em></strong></p>
<a name="MANAGE"></a>
<a name="MANAGE_CT"></a>
<h2>Displaying and managing custom tracks</h2>
<p>
After a custom track has been successfully loaded into the Genome Browser, you can display it -- as
well as manage your entire custom track set -- via the options on the Manage Custom Tracks page.
This page automatically displays when a track has been uploaded into the Genome Browser (see
<a href="#ADD_CT">Loading a Custom Track into the Genome Browser</a>). Alternatively, you can
access the track management page by clicking the "manage custom tracks" button on the
Gateway or Genome Browser annotation tracks pages. (Note that the track management page is available
only if at least one track has been loaded during the current browser session; otherwise, this
button is labeled "add custom tracks" and opens the Add Custom Track page.)</p>
<p>
The table on the Manage Custom Tracks page shows the current set of uploaded custom tracks for the
genome and assembly specified at the top of the page. If tracks have been loaded for more than one
genome assembly, pulldown lists are displayed; to view the uploaded tracks for a different assembly,
select the desired genome and assembly option from the lists.</p>
<p>
The following track information is displayed in the Manage Custom Tracks table:</p>
<ul>
<li>
<strong>Name: </strong> a hyperlink to the Update Custom Track page where you can update your
track configuration and data.</li>
<li>
<strong>Description: </strong>the value of the "description" attribute from the track
line, if present. If no description is included in the input file, this field contains the track
name.</li>
<li>
<strong>Type: </strong>the track type, determined by the Browser based on the format of the
data.</li>
<li>
<strong>Doc: </strong>displays "Y" (Yes) if a description page has been uploaded for the
track; otherwise the field is blank.</li>
<li>
<strong>Items: </strong>the number of data items in the custom track file. An item count is not
displayed for tracks lacking individual items (e.g. wiggle format data).</li>
<li>
<strong>Pos: </strong>the default chromosomal position defined by the track file in either the
browser line "position" attribute or the first data line. Click this link to open the
Genome Browser or Table Browser at the specified position (Note: only the chromosome name is shown
in this column). The Pos column remains blank if the track lacks individual items (e.g. wiggle
format data) and the browser line "position" attribute hasn't been set.</li>
</ul>
<p>
<strong>Displaying a custom track in the Genome Browser</strong><br>
Click the "go" button to display the entire custom track set for the
specified genome assembly in the Genome Browser. By default, the browser will open to the position
specified in the browser line "position" attribute or first data line of the first custom
track in the table, or the last-accessed Genome Browser position if the track is in wiggle data
format. To open the display at the default position for another track in the list, click the track's
position link in the Pos column.</p>
<p>
<strong>Viewing a custom track in the Table Browser</strong><br>
Select "Table Browser" from the drop down menu and click the "go" button to
access the data for the custom track set in the Table Browser. The custom tracks will be listed
in the "Custom Tracks" group pulldown list.</p>
<p>
<strong>Loading additional custom tracks</strong><br>
To load a new custom track into the currently displayed track set, click the "add custom
tracks" button. To change the genome assembly to which the track should be added, select the
appropriate options from the pulldown lists at the top of the page. For instructions on adding a
custom track on the Add Custom Tracks page, see <a href="#ADD_CT">Loading a Custom Track into the
Genome Browser</a>.</p>
<p>
<strong>Removing one or more custom tracks</strong><br>
To remove custom tracks from the uploaded track set, click the checkboxes in the "delete"
column for all tracks you wish to remove, then click the "delete" button. A custom track
may also be removed by clicking the "Remove custom track" button on the track's
description page. Note: removing the track from the Genome Browser does not delete the track file
from your server or local disk.</p>
<p>
<strong>Updating a custom track</strong><br>
To update the stored information for a loaded custom track, click the track's link in the
"Name" column in the Manage Custom Tracks table. A custom track may also be updated by
clicking the "Update custom track" button on the track's description page.</p>
<p>
The Update Custom Track page provides sections for modifying the track configuration information
(the browser lines and track lines), the annotation data, and the descriptive documentation that
accompanies the track. Existing track configuration lines are displayed in the top "Edit
configuration" text box. In the current implementation of this utility, the existing annotation
data is not displayed. Because of this, the data cannot be incrementally edited through this
interface, but instead must be fully replaced using one of the data entry methods described in
<a href="#ADD_CT">Loading a Custom Track into the Genome Browser</a>. If description text has been
uploaded for the track, it will be displayed in the track documentation edit box, where it may be
edited or completely replaced. Once you have completed your updates, click the Submit button to
upload the new data into the Genome Browser.</p>
<p>
If the data or description text for your custom track was originally loaded from a file on your hard
disk or server, you should first edit the file, then reload it from the Update Custom Track page
using the "Choose File" button. Note that edits made on this page to description text uploaded
from a file will not be saved to the original file on your computer or server. Because of this, we
recommend that you use the documentation edit box only for changes made to text that was typed or
pasted in.</p>
<a name="lines"></a>
<h3>Browser lines</h3>
<p>
Browser lines are optional, but they give you control of many aspects of the overall display of the
Genome Browser window when your annotation file
is uploaded. Each line defines one display attribute. Browser lines are in the format:</p>
<p>
<pre><code>browser attribute_name attribute_value(s)</code></pre>
<p>
For example, if the browser line <code>browser position chr22:1-20000</code> is included in the
annotation file, the Genome Browser window will initially display the first 20000 bases of chr
22.</p>
<p>
The following browser line attribute name/value options are available. The value
<em>track_primary_table_name</em> must be set to the name of the primary table on which the
track is based. To identify this table, open up the
<A HREF="../../cgi-bin/hgTables" TARGET=_blank>Table Browser</A>,
select the correct genome assembly, then select the track name from the
<em>track</em> list. The <em>table</em> list will show the primary table.
Alternatively, the primary table name can be obtained from a mouseover on the
track name in the track control section.
You can also find instructions on how to find this table name in the video
"<a href="../../training/vids/index.html#vid06" target="_blank">How do I learn which tables
belong to a data track on the UCSC Genome Browser?</a>".</p>
<p>
Note that composite track subtracks are not valid <em>track_primary_table_name</em> values. To find
the symbolic name of a composite track, look in the <em>tableName</em> field in the <em>trackDb</em>
table, or mouse over the track name in the track control section. It is not possible to display only
a subset of the subtracks at this time.</p>
<p>
Definition: <strong><em><track_primary_table_name(s)></em></strong>. You can find the primary
table name by clicking "View Table Schema" from the track's description page, or from the Table
Browser. It will be listed as the Primary Table. Alternatively, you can mouse-over the track label
in the Browser and look at the URL the link points to. The part after the g= in the URL is the
track's primary table name (e.g., for UCSC Genes you will see g=knownGene in the URL. The track
primary table is knownGene).</p>
<ul>
<li>
<strong>position <<em>position</em>></strong> - Determines the part of the genome that the Genome
Browser will initially open to, in chromosome:start-end format.</li>
<!--
<li>
<strong>pix <<em>width</em>></strong> - Sets the Genome Browser window to the specified width in
pixels.</li>
-->
<li>
<strong>hide all</strong> - Hides all annotation tracks except for those listed in the custom
track file.</li>
<li>
<strong>hide <<em>track_primary_table_name(s)</em>></strong> - Hides the listed tracks.
Multiple track names should be space-separated.</li>
<li>
<strong>dense all</strong> - Displays all tracks in dense mode. NOTE: Use the "all"
option cautiously. If the browser display includes a large number of tracks or a large position
range, this option may overload your browser's resources and cause an error or timeout.</li>
<li>
<strong>dense <<em>track_primary_table_name(s)</em>></strong> - Displays the specified
tracks in dense mode. Symbolic names must be used. Multiple track names should be
space-separated.</li>
<li>
<strong>pack all</strong> - Displays all tracks in pack mode. See NOTE for "dense
all".</li>
<li><strong>pack <<em>track_primary_table_name(s)</em>></strong> - Displays the specified
tracks in pack mode. Symbolic names must be used. Multiple track names should be
space-separated.</li>
<li>
<strong>squish all</strong> - Displays all tracks in squish mode. See NOTE for "dense
all".</li>
<li>
<strong>squish <<em>track_primary_table_name(s)</em>></strong> - Displays the specified
tracks in squish mode. Symbolic names must be used. Multiple track names should be
space-separated.</li>
<li>
<strong>full all</strong> - Displays all tracks in full mode. See NOTE for "dense
all".</li>
<li>
<strong>full <<em>track_primary_table_name(s)</em>></strong> - Displays the specified tracks
in full mode. Symbolic names must be used. Multiple track names should be space-separated.</li>
</ul>
<p>
Note that the Genome Browser will open to the range defined in the Gateway page <em>search term</em>
box or the position saved as the default unless the browser line position attribute is defined in
the annotation file. Although this attribute is optional, it's recommended that you set this value
in your annotation file to ensure that the track will appear in the display range when it is
uploaded into the Genome Browser.</p>
<a name="TRACK"></a>
<h3>Track lines</h3>
<p>
Track lines define the display attributes for all lines in an annotation data set. If more than one
data set is included in the annotation file, each group of data must be preceded by a track line
that describes the display characteristics for that set of data. A track line begins with the word
<code>track</code>, followed by one or more <code>attribute=value</code> pairs. Unlike browser
lines - in which each attribute is defined on a separate line - all of the track attributes for a
given set of data are listed on one line <em>with no line breaks</em>. The inadvertent insertion of
a line break into a track line will generate an error when you attempt to upload the annotation
track into the Genome Browser.</p>
<p>
The following track line attribute=value pairs are defined in the Genome Browser:</p>
<ul>
<li>
<strong>name=<<em>track_label</em>></strong> - Defines the track label that will be displayed to
the left of the track in the Genome Browser window, and also the label of the track control at the
bottom of the screen. The name can consist of up to 15 characters, and must be enclosed in quotes
if the text contains spaces. We recommend that the track_label be restricted to alpha-numeric
characters and spaces to avoid potential parsing problems. The default value is "User
Track".</li>
<li>
<strong>description=<<em>center_label</em>></strong> - Defines the center label of the track in
the Genome Browser window. The description can consist of up to 60 characters, and must be
enclosed in quotes if the text contains spaces. The default value is "User Supplied
Track".</li>
<li>
<strong>type=<<em>track_type</em>></strong> - Defines the track type. The track type attribute is
required for <a href="/FAQ/FAQformat.html#format5.1" target="_blank">BAM</a>,
<a href="/FAQ/FAQformat.html#format1.7" target="_blank">BED detail</a>,
<a href="/FAQ/FAQformat.html#format1.8" target="_blank">bedGraph</a>,
<a href="/FAQ/FAQformat.html#format21" target="_blank">bigBarChart</a>,
<a href="/FAQ/FAQformat.html#format1.5" target="_blank">bigBed</a>,
<a href="/FAQ/FAQformat.html#format9.4" target="_blank">bigChain</a>,
<a href="/FAQ/FAQformat.html#format9.1" target="_blank">bigGenePred</a>,
<a href="/FAQ/FAQformat.html#format22" target="_blank">bigInteract</a>,
<a href="/FAQ/FAQformat.html#format9.5" target="_blank">bigNarrowPeak</a>,
<a href="/FAQ/FAQformat.html#format9.3" target="_blank">bigMaf</a>,
<a href="/FAQ/FAQformat.html#format9.2" target="_blank">bigPsl</a>,
<a href="/FAQ/FAQformat.html#format6.1" target="_blank">bigWig</a>,
<a href="/FAQ/FAQformat.html#format13" target="_blank">broadPeak</a>,
<a href="/FAQ/FAQformat.html#format5.2" target="_blank">CRAM</a>,
<a href="/FAQ/FAQformat.html#format22" target="_blank">interact</a>,
<a href="/FAQ/FAQformat.html#format12" target="_blank">narrowPeak</a>,
<a href="/FAQ/FAQformat.html#format6.5" target="_blank">Microarray</a>,
<a href="/FAQ/FAQformat.html#format10.1" target="_blank">VCF</a> and
<a href="/FAQ/FAQformat.html#format6" target="_blank">WIG</a> tracks.</li>
<li>
<strong>visibility=<<em>display_mode</em>></strong> - Defines the initial display mode of the
annotation track. Values for <em>display_mode</em> include: 0 - hide, 1 - dense, 2 - full, 3 -
pack, and 4 - squish. The numerical values or the words can be used, i.e., full mode may be
specified by "2" or "full". The default is "1".</li>
<li>
<strong>color=<<em>RRR,GGG,BBB</em>></strong> - Defines the main color for the annotation track.
The track color consists of three comma-separated RGB values from 0-255. The default value is
0,0,0 (black).</li>
<li>
<strong>itemRgb=On</strong> - If this attribute is present and is set to "On", the
Genome Browser will use the RGB value shown in the <em>itemRgb</em> field in each data line of
the associated BED track to determine the display color of the data on that line.</li>
<li>
<strong>colorByStrand=<<em>RRR,GGG,BBB RRR,GGG,BBB</em>></strong> - Sets colors for + and -
strands, in that order. The colors consist of three comma-separated RGB values from 0-255 each.
The default is 0,0,0 0,0,0 (both black).</li>
<!--
<li>
<strong>altColor=<<em>RRR,GGG,BBB</em>></strong> - Defines the secondary color for the track.
The alternate color consists of three comma-separated RGB values from 0-255. The default is a
lighter shade of whatever the <em>color</em> attribute is set to.</li>
-->
<li>
<strong>useScore=<<em>use_score</em>></strong> - If this attribute is present and is set to 1,
the <em>score</em> field in each of the track's data lines will be used to determine the level of
shading in which the data is displayed. The track will display in shades of gray unless the
<em>color</em> attribute is set to 100,50,0 (shades of brown) or 0,60,120 (shades of blue). The
default setting for <em>useScore</em> is "0". This table shows the Genome Browser's
translation of BED score values into shades of gray:</p>
<table cellspacing="5">
<tr><td>shade</td>
<td style="background-color: #e2e2e2"> </td>
<td style="background-color: #c6c6c6"> </td>
<td style="background-color: #aaaaaa"> </td>
<td style="background-color: #8d8d8d"> </td>
<td style="background-color: #717171"> </td>
<td style="background-color: #555555"> </td>
<td style="background-color: #383838"> </td>
<td style="background-color: #1c1c1c"> </td>
<td style="background-color: #000000"> </td></tr>
<tr><td>score in range </td>
<td>≤ 166</td>
<td>167-277</td>
<td>278-388</td>
<td>389-499</td>
<td>500-611</td>
<td>612-722</td>
<td>723-833</td>
<td>834-944</td>
<td>≥ 945</td></tr>
</table><br>
<li>
<strong>group=<<em>group</em>></strong> - Defines the annotation track group in which the custom
track will display in the Genome Browser window. By default, <em>group</em> is set to
"user", which causes custom tracks to display at the top of the track listing in the
group "Custom Tracks". The value for "group" <strong>must</strong> be the
"name" of one of the predefined track groups. To get a list of allowable group names for
an assembly, go to the table browser and select "group: All Tables" "table:
grp" and "get output" where entries in the "name" column may be used
and some examples include "genes","regulation" and "rna".<br>
(Note that mirrors may define other group names in the grp table and that the group setting does
not work in track hubs, but does apply for assembly hubs.)</li>
<li>
<strong>priority=<<em>priority</em>></strong> - When the <em>group</em> attribute is set, defines
the display position of the track relative to other tracks within the same group in the Genome
Browser window. If <em>group</em> is not set, the <em>priority</em> attribute defines the track's
order relative to other custom tracks displayed in the default group, "user".</li>
<li>
<strong>db=<<em>UCSC_assembly_name</em>></strong> - When set, indicates the specific genome
assembly for which the annotation data is intended; the custom track manager will display an error
if a user attempts to load the track onto a different assembly. Any valid UCSC assembly ID may be
used (<em>eg.</em> hg18, mm8, felCat1, etc.). The default setting is blank, allowing the custom
track to be displayed on any assembly.</li>
<li>
<strong>offset=<<em>offset</em>></strong> - Defines a number to be added to all coordinates in the
annotation track. The default is "0".</li>
<li>
<strong>maxItems=<<em>#</em>></strong> - Defines the maximum number of items the track can
contain. The default value is 250. Be aware that tracks with an extremely large number of items
can cause system instability. The
<a href="http://genomewiki.ucsc.edu/index.php/Kent_source_utilities" target="_blank"> Kent source
utility</a> bedItemOverlapCount can assist in analyzing base overlap with large tracks.</li>
<li>
<strong>url=<<em>external_url</em>></strong> - Defines a URL for an external link associated with
this track. This URL will be used in the details page for the track. Any "$$"in this
string this will be substituted with the item name. There is no default for this attribute.</li>
<li>
<strong>htmlUrl=<<em>external_url</em>></strong> - Defines a URL for an HTML description page to
be displayed with this track. There is no default for this attribute. A template for a standard
format HTML track description is <a class="change" target="_blank"
href="http://genome.ucsc.edu/goldenPath/help/ct_description.txt">here</a>.</li>
<li>
<strong>bigDataUrl=<<em>external_url</em>></strong> - Defines a URL to the data file for
<a href="../help/bam.html" target="_blank">BAM</a>,
<a href="../help/cram.html" target="_blank">CRAM</a>,
<a href="../help/bigBed.html" target="_blank">bigBed</a>,
<a href="../help/bigWig.html" target="_blank">bigWig</a> or
<a href="../help/vcf.html" target="_blank">VCF</a> tracks. This is a required attribute for those
track types. There is no default for this attribute.</li>
<li>
<strong>doWiggle=<<em>on</em>></strong> - The doWiggle setting enables BAM custom tracks
to be displayed as bar graphs where the height is proportional to the number of reads mapped
to each genomic position. This display is described as a density graph and is best viewed with
the track set to full and scaling set to auto-scale. See the Track Database Definition
<a href="../help/trackDb/trackDbHub.html#doWiggle" target="_blank">doWiggle entry</a>
for more information about the use in hubs and the
<a href="../help/hgBamTrackHelp" target="_blank">configuring BAM tracks</a> and the
<a href="../help/hgWiggleTrackHelp.html" target="_blank">configuring graph-based tracks</a>
help pages to learn how to further change the display.</li>
</ul>
<p>
Here is an example of a properly formatted track line using the bigBed format, with accompanying
browser line:</p>
<pre><code>browser position chr21:33,031,597-33,041,570
track type=bigBed name="bigBed Example One" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</code></pre>
<a name="SHARE"></a>
<h2>Sharing your annotation track with others</h2>
<p>
To make your Genome Browser annotation track viewable by people on other machines or at other sites,
follow the steps below.</p>
<p>
<strong>Step 1.</strong> Put your formatted annotation file on your web site. Be sure that the file
permissions allow it to be read by others.</p>
<p>
<strong>Step 2.</strong> Construct a URL that will link this annotation file to the Genome Browser.
The URL must contain 3 pieces of information specific to your annotation data:</p>
<ul>
<li>
The species or genome assembly on which your annotation data is based. To automatically display
the most recent assembly for a given organism, set the <em>org</em> parameter: <em>e.g.</em>
<code>org=human</code>. To specify a particular genome assembly for an organism, use the
<em>db</em> parameter, <code>db=<databaseName></code>, where <em>databaseName</em> is the UCSC
code for the genome assembly. For a list of these codes, see the Genome Browser
<a href="/FAQ/FAQreleases.html#release1" target="_blank">FAQ</a>. Examples of this include:
db=hg38 (Human Dec. 2013 assembly = GRCh38), db=mm10 (Mouse Dec. 2011 assembly = GRCm38).</li>
<li>Additionally, particular genome assemblies, including assemblies in assembly hubs, can be specified using
the <em>genome</em> parameter, <code>genome=<databaseName></code>, which acts in the same manner as
the <em>db</em> parameter. Here is an example using the house mouse (<i>Mus musculus</i>, 129S1_SvImJ)
assembly hub:
<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt"
target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt</a></li>
<li>
The genome position to which the Genome Browser should initially open. This information is of the
form <code>position=<chrPosition></code>, where <em>chrPosition</em> is a chromosome number, with
or without a set of coordinates. Examples of this include: position=chr22,
position=chr22:15916196-31832390.</li>
<li>
The URL of the annotation file on your web site. This information is of the form
<code>hgt.customText=<url></code>, where <em>url</em> points to the annotation file on your website.
An example of an annotation file URL is <a href="test.bed"
target="_blank">http://genome.ucsc.edu/goldenPath/help/test.bed</a>.</li>
</ul>
<a name="optParams"></a>
<p>
You can add other optional parameters to the URL: (Note: Display may vary if you have conflicting
cart variables, for example having both hide all and highlight features.)
<ul>
<li>
<code>guidelines=on/off</code> - activate or deactivate the blue guidelines -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&guidelines=off"
target="_blank">example link</a> to switch off blue guidelines</li>
<li>
<code>hgFind.matches=<listOfNames></code> - highlight features given their names -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgFind.matches=uc010naf.1,uc011mcz.1"
target="_blank">example link</a> to highlight two transcripts of the ABO gene</li>
<li>
<code>hgt.reset=1</code> - show only the default tracks -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.reset=1"
target="_blank" >example link</a></li>
<li>
<code>hgt.toggleRevCmplDisp=1</code> - show the reverse-complement -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.toggleRevCmplDisp=1"
target="_blank">example link</a> to show the reverse-complement of the ABO gene</li>
<li>
<code>hgt.labelWidth=<number></code> - set the size of the left-side label area -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.labelWidth=50"
target="_blank">example link</a> to increase the label area to 50 characters</li>
<li>
<code>hideTracks=1</code> - hide all tracks -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hideTracks=1"
target="_blank">example link</a> to show no tracks at all</li>
<li>
<code>hideTracks=1&<trackName>=full|dense|pack|hide</code> - hide all tracks and show
other tracks -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hideTracks=1&cytoBand=pack"
target="_blank">example link</a> to show only the Chromosome Bands track and nothing else</li>
<li>
<code>highlight=<db>.<chrom>:<chromStart>-<chromEnd>#<color>|...</code> -
highlight one or more regions in a given color on the image. Note that the arguments have to be
URL-encoded for Internet browsers, so ":" becomes "%3A", "#"
becomes "%23" and "|" becomes "%7"C. -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136136597-136139844&highlight=hg19.chr9%3A136138630-136139650%23AA0000%7Chg19.chr9%3A136136630-136137650%230000FF"
target="_blank">example link</a> to highlight two parts of the ABO locus in red and blue.</li>
<li>
<code>ignoreCookie=1</code> - do not load the user's existing settings saved
in the internet browser's UCSC Genome Browser cookie. This means that the link will show the
Genome Browser default
settings such as track selections, custom tracks, and track hubs. Any changes
you make in this new session will, however, affect the user's settings. E.g.,
if you add a track in this new window, and come back to the genome browser
later, the track will still be there. This setting is useful if a website
wants to link to the Genome Browser, starting with a "clean slate" but
believes the user will come back to the Genome Browser expecting the
changes to still be there.
Compare this behavior to the setting <code>incognito=1</code> described below.
- <a href="../../cgi-bin/hgTracks?db=hg19&ignoreCookie=1"
target="_blank">example link</a> to show the default tracks and positions for hg19,
in a new, clean session.</li>
<li>
- <code>incognito=1</code> - do not load the user's existing settings saved
- in the internet browser's UCSC Genome Browser cookie and also never save them to the cookie.
- This means that that link will show the Genome Browser default
- settings such as track selections, custom
- tracks, and track hubs. Also: Any changes made by the user or other URL arguments
- will not affect the user's
- Genome Browser settings. E.g., if you add a track in this new window, and come
- back to the genome browser later, this track will NOT appear in the new window. This setting
- is useful if a website wants to link to the Genome Browser, wants to start
- with a "clean slate" but does not want any changes to affect other Genome
- Browser windows that are open or that the user may open later.
- - <a href="../../cgi-bin/hgTracks?db=hg19&incognito=1"
- target="_blank">example link</a> to show the default tracks and positions for hg19,
- in a new, clean session,
- that is completely independent from all other Genome Browser windows that the user
- has open or will open later.
- Any changes made to this window will not be saved and are lost as soon as the window is closed.
- Compare this behavior to the setting <code>ignoreCookie=1</code> described above.
- (At the moment,
- there is no visual indicator in such a Genome Browser window that changes are not saved,
- but we could add one
- in the future, please contact us if you think this could be useful for you.)
- This variable is probably
- useful for most websites using our tool hgRenderTracks to show only the
- Browser's main image from a Javascript-driven website.
- </li>
-
<li>
<code>oligoMatch=pack&hgt.oligoMatch=<dnaSeq></code> - switch on the Short Match track and
highlight a matching sequence -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&oligoMatch=pack&hgt.oligoMatch=TATAWAR"
target="_blank">example link</a> to highlight the TATAWAR motif in the ABO locus</li>
<li>
<code>pix=<number></code> - set the width of the image in pixels -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&pix=300"
target="_blank">example link</a> to create a 300-pixel wide image</li>
<li>
<code>textSize=<number></code> - set the size of text font -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&textSize=12"
target="_blank">example link</a> to increase the text font size to 12 pixels</li>
<li>
<code><trackName>=full|pack|dense|hide</code> - show your current tracks, adding a track
and set it to full, pack or dense visibility or hide it, respectively -
<a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&cytoBand=pack"
target="_blank">example link</a> to show the
Chromosome Bands track set to "pack" and added to your view as saved in your cart.
Please note that for this feature to work with
custom tracks you must use the unique name and identifier number
<code>ct_name_####</code> assigned by our system. You can determine the name for a custom track
using the url, <a href = "https://genome.ucsc.edu/cgi-bin/cartDump">
https://genome.ucsc.edu/cgi-bin/cartDump</a>.
<li>
<code><trackName>.heightPer=<number></code> - sets the height of the a bigWig track
in pixels - <a
href="../../cgi-bin/hgTracks?db=hg38&ignoreCookie=1&hideTracks=1&mappability=full&umap24Quantitative.heightPer=100"
target="_blank">example link</a> to set umap bigWig track height to 100 pixels
</li>
<li>
<code><trackName>_hideKids=1</code> - hides a specific super track's individual tracks - <a
href="../../cgi-bin/hgTracks?db=hg19&wgEncodeReg_hideKids=1&ignoreCookie=1" target="_blank">
example link</a> to hide the Encode Regulation super track</li>
<li>
<code><trackName>_sel=1</code> - selects specific subtrack to be 'checked', allowing
display - <a href="../../cgi-bin/hgTracks?db=hg38&refSeqComposite=full&refGene_sel=1" target="_blank">example
link</a> to select the checkbox for UCSC RefSeq subtrack in the refSeq composite track, allowing
display alongside default tracks
</li>
</ul>
<p>
If a login and password is required to access data loaded through a URL (e.g., via https:
protocol), this information can be included in the URL using the format
protocol://user:password@server.com/somepath. Only Basic Authentication is supported for HTTP.
Note that passwords included in URLs are not protected. If a password contains a non-alphanumeric
character, such as $, the character must be replaced by the hexadecimal representation for
that character. For example, in the password mypwd$wk, the $ character should be replaced
by %24, resulting in the modified password mypwd%24wk.</p>
<p>
For integration into your own website e.g. in an html IFRAME, you can obtain the track image only,
without the rest of the genome browser user interface, by replacing hgTracks in the URL with
hgRenderTracks, such as in this example:</p>
<pre><code><a href="http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630"
target="_blank">http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630</a></code></pre>
<p>
Combine the above pieces of information into a URL of the following format (the information
specific to your annotation file is highlighted):</p>
<pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?org=<font color="000099"><em><organismName></em></font>&position=<font color="000099"><em><chrPosition></em></font>&hgt.customText=<font color="000099"><em><url></em></font></code></pre>
<p>
<strong><em>Example #5:</em></strong><br>
The following URL will open up the Genome Browser window to display chr22 of the latest human
genome assembly and will show the annotation track pointed to by the URL
http://genome.ucsc.edu/goldenPath/help/test.bed:
<pre><code
<a class="insideLink" href="../../cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed"
target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed</a></code></pre>
<p>
<strong>Step 3.</strong> Provide the URL to others. To upload a custom annotation track from a
URL into the Genome Browser, paste the URL into the large text edit box on the Add Custom
Tracks page, then click the Submit button.</p>
<p>
If you'd like to share your annotation track with a broader audience, send the URL for your
track—along with a description of the format, methods, and data used—to the UCSC Genome
mailing list
<a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>.
<!-- above address is genome at soe.ucsc.edu -->
<a name="EXAMPLE6"></a>
<p>
<strong><em>Example #6:</em></strong><br>
If you would like to share a URL that your colleague can click on directly, rather than loading it
in the Custom Track tool (as in Example #5), then the URL will need a few extra parameters. Let's
assume that your data is on a server at your institution in one of the large data formats:
<a href="../../FAQ/FAQformat.html#format1.5">bigBed</a>,
<a href="../../FAQ/FAQformat.html#format6.1">bigWig</a>,
<a href="../../FAQ/FAQformat.html#format9.2">bigPsl</a>,
<a href="../../FAQ/FAQformat.html#format21">bigBarChart</a>,
<a href="../../FAQ/FAQformat.html#format9.4">bigChain</a>,
<a href="../../FAQ/FAQformat.html#format22">bigInteract</a>,
<a href="../../FAQ/FAQformat.html#format9.1">bigGenePred</a>,
<a href="../../FAQ/FAQformat.html#format9.3">bigMaf</a>,
<a href="../../FAQ/FAQformat.html#format9.5">bigNarrowPeak</a>,
<a href="../../FAQ/FAQformat.html#format5.1">BAM</a>,
<a href="../../FAQ/FAQformat.html#format5.2">CRAM</a>, or
<a href="../../FAQ/FAQformat.html#format10.1">VCF</a>.
In this case, the URL must include an <code>hgct_customText</code> parameter, which
simulates the text box on the Custom Tracks page. Also, the URL must include
the <code>bigDataUrl</code> that points to the data file on your server.
So, a clickable URL that opens a remote bigBed track for the hg18 assembly to a certain location on
chr21 would look like this:
<pre><code><a href="../../cgi-bin/hgTracks?db=hg18&position=chr21:33038447-33041505&hgct_customText=track%20type=bigBed%20name=myBigBedTrack%20description=%22a%20bigBed%20track%22%20visibility=full%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb"
target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr21:33038447-33041505&hgct_customText<br>
=track%20type=bigBed%20name=myBigBedTrack%20description=%22a%20bigBed%20track%22%20visibility=<br>
full%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb
</code></pre></a>
<p>
Custom Tracks can also be shared with others through named sessions. First, upload your tracks as
discussed in the <a href="#ADD_CT">Loading a Custom Track into the Genome Browser</a> section. Then create a named session that includes your custom tracks by navigating to the "Sessions"
page through the "My Data" section in the menu bar. Once there, follow the instructions in the
<a href=../help/hgSessionHelp.html#Create>Creating a Session</a> section of the Sessions help page.
Once you have saved your custom track into a named session, you can share that session with others
by sharing the URL from the "Browser" link or emailing it to them directly by clicking
the "Email" link.</p>
<p>
<strong>Tip:</strong> Multiple tracks can be placed into one custom track submission. To do so,
create a new file that contains the
<a href="/goldenPath/help/customTrack.html#TRACK">track lines</a> to each file that will be
included. To submit this custom set of tracks, merely use the URL to this new file.</p>
<a name="TROUBLE"></a>
<h2>Troubleshooting annotation display problems</h2>
<p>
Occasionally users encounter problems when uploading annotation files to the Genome Browser. In
most cases, these problems are caused by errors in the format of the annotation file and can be
tracked down using the information displayed in the error message. This section contains suggestions
for resolving common display problems. If you are still unable to successfully display your
data, please contact
<a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>
<!-- above address is genome at soe.ucsc.edu -->
for further assistance.
<strong><span class="gbsWarnText">Messages sent to this address will be posted to the moderated genome mailing list, which is
archived on a SEARCHABLE, PUBLIC</span>
<a HREF="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">Google Groups
forum</a></strong>.</p>
<p>
<strong><em>Problem: </em></strong>When I try one of your examples by cutting and pasting it into
the Genome Browser, I get an error message.<br>
<strong><em>Solution: </em></strong>Check that none of the browser lines, track lines, or data lines
in your annotation file contains a line break. If the example contains GFF or GTF data lines, check
that all the fields are tab-separated rather than space-separated.</p>
<p>
<strong><em>Problem:</em></strong> When I click the <em>submit</em> button, I get the error message "line 1 of custom input:".<br>
<strong><em>Solution:</em></strong> Check that none of the browser lines, track lines, or data
lines in your annotation file contains a line break. A common source for this problem is the track
line: all of the attribute pairs must on the same line and must not be separated by a line break.
If you are uploading your annotation file by pasting it into the text box on the Genome Browser
Gateway page, check that the cut-and-paste operation did not inadvertently insert unwanted line
feeds into the longer lines.</p>
<p>
<strong><em>Problem:</em></strong> When I click the <em>submit</em> button, I get the error message
"line # of custom input: missing = in var/val pair".<br>
<strong><em>Solution:</em></strong> Check for incorrect syntax in the track lines in the annotation
file. Be sure that each track line attribute pair consists of the format
<em>attribute=attribute name</em>.</p>
<p>
<strong><em>Problem:</em></strong> When I click the <em>submit</em> button, I get the error message
"line # of custom input: BED chromStarts[i] must be in ascending order".<br>
<strong><em>Solution:</em></strong> This is most likely caused by a logical conflict in the Genome
Browse software. It accepts custom GFF tracks that have multiple "exons" at the same
position, but not BED tracks. Because the browser translates GFF tracks to BED format before
storing the custom track data, GFF tracks with multiple exons will case an error when the BED is
read back in. To work around this problem, remove duplicate lines in the GFF track.</p>
<p>
<strong><em>Problem:</em></strong> When I click the <em>submit</em> button, the Genome Browser
track window displays OK, but my track isn't visible.<br>
<strong><em>Solution:</em></strong> Check the browser and track lines in your annotation file to
make sure that you haven't accidentally set the display mode for the track to <em>hide</em>. If you
are using the Annotation File box on the Genome Browser Gateway page to upload the track, check that
you've entered the correct file name. If neither of these is the cause of the problem, try resetting
the Genome Browser to clear any settings that may be preventing the annotation to display. To reset
the Genome Browser, click the <em>Click here to reset</em> link on the Gateway page. If the
annotation track still doesn't display, you may need to clear the cookies in your Internet browser
as well (refer to your Internet browser's documentation for further information).</p>
<p>
<strong><em>Problem:</em></strong> I am trying to upload some custom tracks (.gz files) to the
Genome Browser using a URL from a GEO query. However, the upload is failing with the error
"line 1 of <filename>.gz: thickStart after thickEnd".<br>
<strong><em>Solution:</em></strong> The custom track mechanism supports plain BED files (not bigBed)
that are of the type <a href="../../FAQ/FAQformat.html#format13">broadPeak</a> or
<a href="../../FAQ/FAQformat.html#format12">narrowPeak</a>. Set the track attribute
<a href="#TRACK">type=<<em>track_type</em>></a> to enable the loader to correctly process the
special columns at the end of each line. Your track type entry should consist of two lines: the
first to define the track type and the second to specify the URL. For example:</p>
<pre><code>track type=<font color="000099">broadPeak</font>
https://www.ncbi.nlm.nih.gov/geosuppl/...</code></pre>
<p>
<strong><em>Problem:</em></strong> I've gotten my annotation track to display, but now I can't make
it go away! How do I remove an annotation track from my Genome Browser display?<br>
<strong><em>Solution:</em></strong> To remove only one track, click the <em>Manage Custom
Tracks</em> button and delete the desired track using the checkbox and Delete button. To quickly
remove all of your custom tracks, reset the Genome Browser to its default settings by clicking the
<em>Click here to reset</em> link on the Gateway page. Note that this reset will also remove any
other customizations you have made to your Genome Browser display.</p>
<p>
<strong><em>Problem:</em></strong> I put my custom track files on Dropbox,
Apple iCloud, Google Drive, Amazon Drive, Box.com, Microsoft OneDrive, or
another "online cloud backup" provider and they will not display in the browser.
Why? <br>
<em>OR</em><br>
<strong><em>Problem:</em></strong> When I try to visualize my custom tracks in the Browser, I
receive the error message "Byte-range request was ignored by server".<br>
<strong><em>Solution:</em></strong> Backup providers used to work for hosting
simple text-based custom tracks, but things have changed. For large custom track data sets, the use
of indexed binary formats such as bigBed and bigWig is preferable and usually fail with backup providers.
These formats provide much faster display performance
because only the portion of the file needed to display the currently viewed region must be
transferred to the Genome Browser server. This requires that they are stored on a real web server.
And to allow this type of display, byte-range support must be
enabled on the web server. No commercial online backup solution supports this,
to our knowledge. To check if your server has byte-range requests enabled,
issue the following command:</p>
<pre><code> curl -I <URL of your file></code></pre>
<p>
In order for your server to host bigBed and bigWig files (or track hubs) for Genome Browser display,
the command output must contain:
<pre><code>Accept-Ranges: bytes</code></pre>
<p>
If you do not receive this output, you may be able to resolve the problem through one of the
following actions:</p>
<ul>
<li>
Store the files on a real web server, e.g. at your University. Check with the
systems administrators about the configuration of the server. This will often
solve the problem.</li>
<li>
Find another site with a server that supports byte-ranges.</li>
<li>
Install an Apache alternative http server such as Cherokee.</li>
</ul>
<p>
<strong><em>Problem:</em></strong> I used to host files on Dropbox which used to accept byte-range
requests, but I can't get my data to display. Why?<br>
<strong><em>Solution:</em></strong> As described in the previous question, Dropbox is a backup provider
and not a real web server and as such does not support hosting indexed files, even though it used to
work to some extent. Dropbox recently removed their Public Folder feature, which means all links
to files hosted there are inaccessible to the browser. For more information, please refer to <a
href="https://www.dropbox.com/help/files-folders/public-folder" target="_blank">this announcement
</a>.</p>
<a name="BYTERANGE"></a>
<p>
<strong><em>Problem:</em></strong> If I can't host files on backup providers
like Dropbox or Google Drive where can I host my files, especially my bigWigs
and bigBeds?<br>
<strong><em>Solution:</em></strong> The NSF-funded website <a href="http://cyverse.org">CyVerse</a>
was created to provide free hosting services to researchers, and allows byte-range
requests, meaning binary files such as BAMs, bigBeds, and bigWigs can be hosted. Please see the
<a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub help page for more
information on hosting your data at CyVerse and other alternatives.</p>
<p>
<strong><em>Problem:</em></strong> I have a bigBed file with colors in the 9th column. I set the
option itemRgb on in the trackDb file, the track is fine, but why are the boxes all black?<br>
<strong><em>Solution:</em></strong> When type is set to bigBed, the track hub assumes that the
bigBed track is BED3 by default. To allow track hubs to use all fields in a bigBed file, you must
define how many columns to expect. For example, if a bigBed file has nine columns, which would
include an itemRgb field to display a R,G,B color value (e.g. 255,0,0), specify the type
as <code>type bigBed 9</code> or if the bigBed contains additional <a href="../../FAQ/FAQformat.html#format1"
target="_blank">non-standard columns</a>, use <code>type bigBed 9 +</code>.</p>