Displaying Your Own Annotations in the Genome Browser
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 Session.
Optionally, users can make custom annotations viewable by others as well.
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. Many individuals and labs have contributed
custom tracks to the Genome Browser website for use by others. To view a list
of these custom annotation tracks, click the
Custom Tracks link on
the Genome Browser home page.
Custom annotation tracks are similar to standard tracks, but never become part
of the MySQL genome database. Each track has its own controller and persists
even when not displayed in the Genome Browser window, e.g. if the position
changes to a range that no longer includes the track. Typically, custom
annotation tracks are aligned under corresponding genomic sequence, but they
can also be completely unrelated to the data. For example, a track can be
displayed under a long sequence consisting of millions of Ns.
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.
To construct an annotation file and display it in the Genome
Browser, follow these steps:
Step 1. Format the data set
Formulate your data set as a tab-separated file using one of the formats
supported by the Genome Browser. Annotation data can be in
standard GFF format or in
a format designed specifically for the Human Genome Project or UCSC Genome
Personal Genome SNP,
GFF and GTF files must be tab-delimited rather than
space-delimited to display correctly.
Chromosome references must be of the form chrN (the parsing of
chromosome names is case-sensitive).
You may include more than one data
set in your annotation file; these need not be in the same
Step 2. Define the Genome Browser display characteristics
Add one or more optional browser lines 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.
Step 3. Define the annotation track display characteristics
Following the browser lines--and immediately preceding the formatted
data--add a track line 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 type=<track_type> 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.
Here is an example of a simple annotation file that contains a list of
browser position chr22:20100000-20100900
track name=coords description="Chromosome coordinates list" visibility=2
chr22 20100000 20100100
chr22 20100011 20100200
chr22 20100215 20100400
chr22 20100350 20100500
chr22 20100700 20100800
chr22 20100700 20100900
Click here to view this track in the Genome Browser.
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 chr 22.
The second track displays red 100-base features alternating with
blank space in the same region of chr 22.
browser position chr22:20100000-20140000
track name=spacer description="Blue ticks every 10000 bases" color=0,0,255,
chr22 20100000 20100001
chr22 20110000 20110001
chr22 20120000 20120001
track name=even description="Red ticks every 100 bases, skip 100" color=255,0,0
chr22 20100000 20100100 first
chr22 20100200 20100300 second
chr22 20100400 20100500 third
Click here to view this track in the Genome Browser.
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. NOTE: The track name line in this example
has been split over 2 lines for documentation purposes.
If you paste this example into the Genome Browser, you must remove the line
break to display the track successfully.
Click here for a copy of this
example that can be pasted into the browser without editing.
browser position chr22:1000-10000
browser hide all
track name="BED track" description="BED format custom track example" visibility=2
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
here to view this track in the Genome Browser.
Step 4. Display your annotation track in the Genome Browser
To view your annotation data in the Genome Browser, open the
Genome Browser home page and click the Genome
Browser link in the top menu bar. On the
Gateway page that
displays, select the genome and assembly on which your annotation data is based,
then click the "add custom tracks" button. (Note: if the Gateway
displays the "manage custom tracks" button instead, see
Displaying and Managing Custom Tracks for
information on how to display your track.)
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 type=<track_type>
attribute is required for some tracks. For more information on these methods, as
well as information on creating and adding track documentation, see
Loading a Custom Track into the Genome Browser.
If you encounter difficulties displaying your annotation, read the section
Troubleshooting Annotation Display Problems.
Step 5. (Optional) Add details pages for individual track features
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.
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 url attribute.
In the annotation file, set the url attribute in the track line to point
to a publicly available page on a web server. The url attribute
substitutes each occurrence of '$$' in the URL string with the name defined by the
name attribute. You can take advantage of this feature to provide
individualized information for each feature in your track by creating HTML anchors
that correspond to the feature names in your web page.
Here is an example of a file in which the url attribute has been set to
point to the file http://genome.ucsc.edu/goldenPath/help/clones.html. The '#$$'
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.).
NOTE: The track line in this example has been split over 2 lines for
documentation purposes. If you paste this example into
the browser, you must remove the line break to display the track successfully.
Click here for a copy of this
example that can be pasted into the browser without editing.
browser position chr22:10000000-10020000
browser hide all
track name=clones description="Clones" visibility=2
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
here to display this track in the Genome Browser.
Step 6. (Optional) Share your annotation track with others
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 Sharing Your Annotation Track with
Loading a Custom Track into the Genome Browser
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.
To load a custom track into the Genome Browser:
Step 1. Open the Add Custom Tracks page
Click the "add custom tracks" button on the Genome Browser
Gateway page. (Note: if one or more tracks
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
Gateway page will be labeled "manage custom tracks" and will
automatically direct you to the track management page. See
Displaying and Managing Custom Tracks for more
Step 2. Load the custom track data
The Add Custom Tracks page contains separate
sections for uploading custom track data and optional custom track
Load the annotation data into the upper section by one of the following
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
type=<track_type> required for some tracks,
for example such as "track type=broadPeak".
Click the "Browse" 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 (.gz), compress (.Z), or bzip2 (.bz2).
Files containing compressed data must include the appropriate suffix in their
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.
Multiple custom tracks may be uploaded at one time on the Add Custom Tracks
page through one of the following methods:
Step 3. (Optional) Load the custom track description page
Put all the tracks into the same file (rather than separate files), then
load the file via the Browse button.
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 data box.
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:
Click the "Browse" button directly above the documentation text box,
then choose a text file from your local computer, or type the pathname of the
file into the "upload" text box adjacent to the "Browse"
Paste or type the custom track data directly into the data 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.
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":
In this case, there is no need to insert anything into the documentation text
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 template
that may be copied and pasted into a file for editing.
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.
Step 4. Upload the track
Click the Submit 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 Troubleshooting
Annotation Display Problems for help in diagnosing custom track problems.
Displaying and Managing Custom Tracks
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
Loading a Custom Track into the Genome Browser).
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.)
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.
The following track information is displayed in the Manage Custom Tracks
- Name: a hyperlink to the Update Custom Track page where you can
update your track configuration and data.
- Description: 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.
- Type: the track type, determined by the Browser based on the format
of the data.
- Doc: displays "Y" (Yes) if a description page has been uploaded for
the track; otherwise the field is blank.
- Items: 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
- Pos: 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.
Displaying a custom track in the Genome Browser
Click the "go to genome browser" 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.
Viewing a custom track in the Table Browser
Click the "go to table browser" 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
Loading additional custom tracks
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
Loading a Custom Track into the Genome Browser.
Removing one or more custom tracks
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.
Updating a custom track
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.
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 Loading a Custom Track
into the Genome Browser. 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.
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 "Browse" 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.
Browser lines configure the overall display of the Genome Browser
window when your annotation file is uploaded. Each line defines one display
attribute. Browser lines consist of the format:
browser attribute_name attribute_value(s)
For example, if the browser line browser
position chr22:1-20000 is included in the annotation file, the Genome
Browser window will initially display the first 20000 bases of chr 22.
The following browser line attribute name/value options are available.
The value track_name must be set to the name of the primary table
on which the the track is based. To identify this table, open up the
select the correct genome assembly, then select the track name from the
track list. The table 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.
Note that composite track subtracks are not valid track_name
values. To find the symbolic name of a composite track, look in the
tableName field in the trackDb table, or mouseover the track
name in the track control section. It is not possible to display only a subset
of the subtracks at this time.
- position <position> - Determines the part of the genome
that the Genome Browser will initially open to, in chromosome:start-end format.
- hide all - Hides all annotation tracks except for those listed
in the custom track file.
- hide <track_primary_table_name(s)> - Hides the listed tracks.
Multiple track names should be space-separated.
- dense all - 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.
- dense <track_primary_table_name(s)> - Displays the specified tracks in
dense mode. Symbolic names must be used. Multiple track names should be
- pack all - Displays all tracks in pack mode. See NOTE for
- pack <track_primary_table_name(s)> - Displays the specified tracks in
pack mode. Symbolic names must be used. Multiple track names should be
- squish all - Displays all tracks in squish mode. See NOTE for
- squish <track_primary_table_name(s)> - Displays the specified tracks in
squish mode. Symbolic names must be used. Multiple track names should be
- full all - Displays all tracks in full mode. See NOTE for
- full <track_primary_table_name(s)> - Displays the specified tracks in
full mode. Symbolic names must be used. Multiple track names should be
Definition: <track_primary_table_name(s)>. 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).
Note that the Genome Browser will open to the range defined in the
Gateway page search term 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.
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 track, followed by one or
more attribute=value 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 with no line
breaks. 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.
The following track line attribute=value pairs are defined in the
- name=<track_label> - 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".
- description=<center_label> - 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".
- type=<track_type> - Defines the track type. The track type
attribute is required for
- visibility=<display_mode> - Defines the
initial display mode of the annotation track. Values for
display_mode 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".
- color=<RRR,GGG,BBB> - 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).
- itemRgb=On - If this attribute is present and is set to
"On", the Genome Browser will use the RGB value shown in
the itemRgb field in each data line of
the associated BED track to determine the display color of the data on
- colorByStrand=<RRR,GGG,BBB RRR,GGG,BBB> - 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).
- useScore=<use_score> - If this attribute is
present and is set to 1, the score 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 color attribute is set to 100,50,0 (shades of brown) or
0,60,120 (shades of blue). The default setting for useScore is "0".
This table shows the Genome Browser's translation of BED score values into
shades of gray:
|score in range
- group=<group> - Defines the annotation track group
in which the custom track will display in the Genome Browser window.
By default, group 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" must 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". Entries in the "name" column may be used.
(Note that mirrors may define other group names in the grp table.)
- priority=<priority> - When the group
attribute is set, defines the display position of the track relative
to other tracks within the same group in the Genome Browser window.
If group is not set, the priority attribute defines
the track's order relative to other custom tracks displayed in the
default group, "user".
- db=<UCSC_assembly_name> - 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 (eg. hg18, mm8, felCat1, etc.). The default setting
is blank, allowing the custom track to be displayed on any assembly.
- offset=<offset> - Defines a number to be added
to all coordinates in the annotation track. The default is "0".
- maxItems=<#> - 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
Kent source utility bedItemOverlapCount can assist in analyzing base
overlap with large tracks.
- url=<external_url> - 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.
- htmlUrl=<external_url> - 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
- bigDataUrl=<external_url> - Defines a URL to the
data file for
tracks. This is a required attribute for those track types. There is no
default for this attribute.
Sharing Your Annotation Track with Others
To make your Genome Browser annotation track viewable by people on
other machines or at other sites, follow the steps below. (Note that
some of the URL examples in this section have been broken up into 2
lines for documentation display purposes).|
Put your formatted annotation file on your web site. Be sure that
the file permissions allow it to be read by others.
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:
- 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 org parameter: e.g. org=human. To specify a
particular genome assembly for an organism, use the db parameter,
db=database_name, where database_name is the UCSC code for
the genome assembly. For a list of these codes, see the Genome Browser FAQ.
Examples of this include: db=hg16 (Human July 2003 assembly), db=mm6
(Mouse Mar. 2005 assembly).
- The genome position to which the Genome Browser should initially
open. This information is of the form
position=chr_position, where chr_position is a
chromosome number, with or without a set of
coordinates. Examples of this include: position=chr22, position=chr22:15916196-31832390.
- The URL of the annotation file on your web site. This information is
of the form hgt.customText=URL, where
URL points to the annotation file on your website. An example of an
annotation file URL is http://genome.ucsc.edu/goldenPath/help/test.bed.
- 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:email@example.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.
Combine the above pieces of information into a URL of the following
format (the information specific to your annotation file is highlighted):
The following URL will open up the Genome Browser
window to display chr 22 of the latest human genome assembly
and will show the annotation track pointed to by the URL
Step 3. Provide the URL to others. To upload a custom annotation track
pointed to by 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.
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
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 10), 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:
In this case, the URL must include an hgct_customText parameter, which
simulates the text box on the Custom Tracks page. Also, the URL must include
the bigDataUrl 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:
Tip: Multiple tracks can be placed into one custom track submission. To do so, create
a new file that contains the track lines
to each file that will be included. To submit this custom set of tracks, merely use the URL to
this new file.
Troubleshooting Annotation Display Problems
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
for further assistance.
Messages sent to this address will be posted to the moderated genome mailing
list, which is archived on a public Web-accessible pipermail archive.
This archive may be indexed by non-UCSC sites such as Google.
Problem: When I try one of your examples by cutting and pasting
it into the Genome Browser, I get an error message.
Solution: 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.
Problem: When I click the submit button, I get
the error message "line 1 of custom input:".
Solution: 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
did not inadvertently insert unwanted line feeds into the longer lines.
Problem: When I click the submit button, I get the
error message "line # of custom input: missing = in var/val pair".
Solution: Check for incorrect syntax in the track
lines in the annotation file. Be sure that each track line
attribute pair consists of the format attribute=attribute name.
Problem: When I click the submit button, I get the
error message "line # of custom input: BED chromStarts[i] must be in ascending order".
Solution: 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.
Problem: When I click the submit button, the Genome Browser
track window displays OK, but my track isn't visible.
Solution: 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 hide. 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 Click here to reset 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).
Problem: I am trying to upload some custom tracks (.gz files)
to the genome browser using a URL from a GEO query. However it is not
uploading and I receive the errror "line 1 of somefile.gz: thickStart after thickEnd".
Solution: The custom track mechanism supports plain BED files
(not bigBed) that are of the type broadPeak or
narrowPeak. If you supply
the track type=<track_type> attribute
then the loader will understand the special columns at the end of
each line. Your entry should be two lines, the first to define the track type
and the second for the URL. For example:
Problem: 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?
Solution: Reset the Genome Browser by clicking the
Click here to reset link on the Gateway page. This should reset
your Genome Browser display to its default settings and remove all your
custom tracks. To remove only one track of several, click the Manage
Custom Tracks button and delete the track using the checkbox and Delete