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 Browser, including 
bedGraph,
GTF, PSL, BED, 
bigBed, WIG, 
bigWig, 
BAM,
VCF,
MAF, 
BED detail,
Personal Genome SNP,
and microarray
(BED15). 
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
format. 
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. 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.
Example 1:
Here is an example of a simple annotation file that contains a list of
chromosome coordinates. 
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.
Example 2:
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.
Example 3:
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
color=0,128,0 useScore=1
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
Click 
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. 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 '$$' in the URL string with the name defined by the 
name attribute. You can take advantage of this feature to provide 
individualized information for each feature in your track by creating HTML anchors 
that correspond to the feature names in your web page.
Example 4:
Here is an example of a file in which the url attribute has been set to
point to the file http://genome.ucsc.edu/goldenPath/help/clones.html. The '#$$'
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
color=0,128,0 useScore=1 
url="http://genome.ucsc.edu/goldenPath/help/clones.html#$$"
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 
Click 
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
Others.
	 | 
	
        
	
        
        | | | 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 pageClick the "add custom tracks" button on the Genome Browser
Gateway page. (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 
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 
information.)
 
Step 2. Load the custom track dataThe 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:
 
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.
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 
names.
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"
button.
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": 
htmlUrl=<external_url>. 
In this case, there is no need to insert anything into the documentation text 
box.
 
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 trackClick 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.
 |  | 
 
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        | | | 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 
table:
 
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 
data). 
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 BrowserClick 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 BrowserClick 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
list.
 
Loading additional custom tracksTo 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 tracksTo 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 trackTo 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.
         |  | 
 
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  	| | |  | 
|---|
 |  | 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 
Table Browser, 
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_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_name(s)> - Displays the specified tracks in
   dense mode. Symbolic names must be used. Multiple track names should be
   space-separated. 
   pack all - Displays all tracks in pack mode. See NOTE for 
   "dense all".
   pack <track_name(s)> - Displays the specified tracks in
   pack mode. Symbolic names must be used. Multiple track names should be 
   space-separated. 
   squish all - Displays all tracks in squish mode. See NOTE for 
   "dense all".
   squish <track_name(s)> - Displays the specified tracks in
   squish mode. Symbolic names must be used. Multiple track names should be 
   space-separated. 
   full all - Displays all tracks in full mode. See NOTE for 
   "dense all".
   full <track_name(s)> - Displays the specified tracks in
   full mode. Symbolic names must be used. Multiple track names should be 
   space-separated. 
 
Note that the Genome Browser will open to the range defined in the
Gateway page position or 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
Genome Browser: 
	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".
	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
	that line.
       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:
| 
    | shade |  |  |  |  |  |  |  |  |  |  | score in range | ≤ 166 | 167-277 | 278-388 | 389-499 | 500-611 | 612-722 | 723-833 | 834-944 | ≥ 945 |  | 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 window.
	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".
	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 
        
        here.
 |  | 
 
 | 
 | 
	
	
  	
  	| | |  | 
|---|
 |  | BED format provides a flexible way to define the data lines that
are displayed in an annotation track. BED lines have three required fields and 
nine additional optional fields. The number of fields per line must be consistent
throughout any single set of data in an annotation track.  The order of the
optional fields is binding: lower-numbered fields must always be populated if
higher-numbered fields are used.
 If your data set is BED-like, but it is very large and you would like to 
keep it on your own server, you should use the bigBed
data format. 
 The first three required BED fields are: 
	chrom - The name of the chromosome (e.g. chr3, chrY,
	chr2_random) or scaffold (e.g. scaffold10671).
	chromStart - The starting position of the feature in the
	chromosome or scaffold. The first base in a chromosome is numbered 0.
	chromEnd - The ending position of the feature in the
	chromosome or scaffold. The chromEnd base is not included in the
	display of the feature. For example, the first 100 bases of a
	chromosome are defined as chromStart=0, chromEnd=100, and span
	the bases numbered 0-99.
 The 9 additional optional BED fields are: 
	name - Defines the name of the BED line.  This label is
	displayed to the left of the BED line in the Genome Browser
	window when the track is open to full display mode or directly to the
	left of the item in pack mode. 
	score - A score between 0 and 1000. If the track line 
	useScore attribute is set to 1 for this annotation data set, the
	score value will determine the level of gray in which
	this feature is displayed (higher numbers = darker gray).
        This table shows the Genome Browser's translation of BED score values into
        shades of gray:
| 
    | shade |  |  |  |  |  |  |  |  |  |  | score in range | ≤ 166 | 167-277 | 278-388 | 389-499 | 500-611 | 612-722 | 723-833 | 834-944 | ≥ 945 |  | strand - Defines the strand - either '+' or '-'.
	thickStart - The starting position at which the feature
	is drawn thickly (for example, the start codon in gene
	displays).
	thickEnd - The ending position at which the feature is
	drawn thickly (for example, the stop codon in gene displays).
	itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0).
	If the track line itemRgb attribute is set to "On",
	this RBG value will determine the display color of the data contained
	in this BED line. NOTE: It is recommended that a simple color scheme 
	(eight colors or less) be used with this attribute to avoid overwhelming
	the color resources of the Genome Browser and your Internet browser. 
	blockCount - The number of blocks (exons) in the
	BED line.
	blockSizes - A comma-separated list of the block
	sizes. The number of items in this list should correspond to
	blockCount.
	blockStarts - A comma-separated list of block starts.
	All of the blockStart positions should be calculated relative to
	chromStart. The number of items in
	this list should correspond to blockCount.
 
See Example 3 for a demonstration of a custom track that uses a 
complete BED12 definition. Example 5:This example shows an annotation track that uses the itemRgb attribute to 
individually color each data line. In this track, the color scheme distinguishes
between items named "Pos*" and those named "Neg*". See the 
usage note in the itemRgb description above for color palette 
restrictions.
NOTE: The track and data lines in this example have been reformatted for 
documentation purposes. Click here 
for a copy of this example that can be pasted into the browser without editing.
 
 browser position chr7:127471196-127495720
browser hide all
track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 
itemRgb="On" 
chr7	127471196  127472363  Pos1  0  +  127471196  127472363  255,0,0
chr7	127472363  127473530  Pos2  0  +  127472363  127473530  255,0,0
chr7	127473530  127474697  Pos3  0  +  127473530  127474697  255,0,0
chr7	127474697  127475864  Pos4  0  +  127474697  127475864  255,0,0
chr7	127475864  127477031  Neg1  0  -  127475864  127477031  0,0,255
chr7	127477031  127478198  Neg2  0  -  127477031  127478198  0,0,255
chr7	127478198  127479365  Neg3  0  -  127478198  127479365  0,0,255
chr7	127479365  127480532  Pos5  0  +  127479365  127480532  255,0,0
chr7	127480532  127481699  Neg4  0  -  127480532  127481699  0,0,255
Click 
here to display this track in the Genome Browser. Example 5b:It is also possible to color items by strand in a BED track 
using the colorByStrand attribute in the 
track line as shown below. For BED 
tracks, this attribute functions only for custom tracks 
with 6 to 8 fields (i.e. BED6 through BED8).
NOTE: The track and data lines in this example have been reformatted for
documentation purposes. Click here
for a copy of this example that can be pasted into the browser without editing.
 
 browser position chr7:127471196-127495720
browser hide all
track name="ColorByStrandDemo" description="Color by strand demonstration" 
visibility=2 colorByStrand="255,0,0 0,0,255"
chr7    127471196  127472363  Pos1  0  +
chr7    127472363  127473530  Pos2  0  +
chr7    127473530  127474697  Pos3  0  +
chr7    127474697  127475864  Pos4  0  +
chr7    127475864  127477031  Neg1  0  -
chr7    127477031  127478198  Neg2  0  -
chr7    127478198  127479365  Neg3  0  -
chr7    127479365  127480532  Pos5  0  +
chr7    127480532  127481699  Neg4  0  -
Click
here to display this track in the Genome Browser. |  | 
 
 | 
 | 
	
	
  	
  	| | |  | 
|---|
 |  | PSL lines represent alignments, and are typically taken from files generated by BLAT 
or psLayout. See the 
BLAT 
documentation for more details. All of the following fields are
required on each data line within a PSL file:
 
matches - Number of bases that match that aren't repeats
misMatches - Number of bases that don't match
repMatches - Number of bases that match but are part of repeats
nCount - Number of 'N' bases
qNumInsert - Number of inserts in query
qBaseInsert - Number of bases inserted in query
tNumInsert - Number of inserts in target
tBaseInsert - Number of bases inserted in target
strand - '+' or '-' for query strand. In protein or translated alignments, the second '+'or '-' is for genomic strand
qName - Query sequence name
qSize - Query sequence size
qStart - Alignment start position in query
qEnd - Alignment end position in query
tName - Target sequence name
tSize - Target sequence size
tStart - Alignment start position in target
tEnd - Alignment end position in target
blockCount - Number of blocks in the alignment
blockSizes - Comma-separated list of sizes of each block
qStarts - Comma-separated list of starting positions of each block in query
tStarts - Comma-separated list of starting positions of each block in target
 Example 6:Here is an example of an annotation track in PSL format. Note that line
breaks have been inserted into this example for
documentation display purposes. Click here for a copy of this example that can be pasted into the 
browser without editing.
 
browser position chr22:13073000-13074000  
browser hide all
track name=fishBlats description="Fish BLAT" visibility=2
useScore=1
59 9 0 0 1 823 1 96 +- FS_CONTIG_48080_1 1955 171 1062 chr22 
    47748585 13073589 13073753 2 48,20,  171,1042,  34674832,34674976,
59 7 0 0 1 55 1 55 +- FS_CONTIG_26780_1 2825 2456 2577 chr22 
    47748585 13073626 13073747 2 21,45,  2456,2532,  34674838,34674914,
59 7 0 0 1 55 1 55 -+ FS_CONTIG_26780_1 2825 2455 2676 chr22 
    47748585 13073727 13073848 2 45,21,  249,349,  13073727,13073827,
Click 
here to display this track in the Genome Browser.Be aware that the coordinates for a negative strand in a PSL 
line are handled in a special way. In the 
qStart and qEnd fields, the coordinates indicate 
the position where the query matches from 
the point of view of the forward strand, even when the match is on the reverse strand.
However, in the qStarts list, the coordinates are reversed. 
Example 7:Here is a 30-mer containing 2 blocks that align on the minus strand and 
2 blocks that align on the plus strand (this sometimes can happen in response to 
assembly errors):
 
 
 
| 0         1         2         3 tens position in query    |  | 0123456789012345678901234567890 ones position in query    |  |             ++++          +++++ plus strand alignment on query    |  |     --------    ----------      minus strand alignment on query    |  |  |  |  |  | Plus strand:    |  |      qStart=12  |  |      qEnd=31  |  |      blockSizes=4,5  |  |      qStarts=12,26    |  |                        |  | Minus strand:    |  |      qStart=4  |  |      qEnd=26  |  |      blockSizes=10,8  |  |      qStarts=5,19     |  Essentially, the minus strand blockSizes and qStarts are 
what you would get if you reverse-complemented the query.
However, the qStart and qEnd are not reversed. To convert one to the other:
 
     qStart = qSize - revQEnd
     qEnd = qSize - revQStart
 |  | 
 
 | 
 | 
	
  	
  	| | |  | 
|---|
 |  | GFF (General Feature Format) lines are based on the GFF standard file format.  GFF 
lines have nine required fields that must be tab-separated. If the fields are 
separated by spaces instead of tabs, the track will not display correctly. For more
information on GFF format, refer to http://www.sanger.ac.uk/Software/formats/GFF.  
Here is a brief description of the GFF fields: 
	seqname - The name of the sequence.  Must be a chromosome or scaffold.
	source - The program that generated this feature.
	feature - The name of this type of feature. Some examples of
	standard feature types are "CDS", "start_codon", "stop_codon", and
	"exon".  
	start - The starting position of the feature in the sequence.  
	The first base is numbered 1.
	end - The ending position of the feature (inclusive).
	score - A score between 0 and 1000. If the track line 
	useScore attribute is set to 1 for this annotation data set, the
	score value will determine the level of gray in which
	this feature is displayed (higher numbers = darker gray). If there is no
	score value, enter ".".
	strand - Valid entries include '+', '-', or '.' (for don't know/don't care).
	frame - If the feature is a coding exon, frame should 
	be a number between 0-2 that represents the reading frame of the
	first base.  If the feature is not a coding exon, the value should be '.'.
	group - All lines with the same group are linked together into a single item.
 Example 8:Here's an example of a GFF-based track. 
Click here for a copy of this 
example that can be pasted into the browser without editing. 
NOTE: Paste operations on some platforms will replace tabs with spaces, which
will result in an error when the GFF track is uploaded. If you encounter an
error when loading a GFF track, check that the data lines contain tabs rather
than spaces.
 browser position chr22:10000000-10020000  
browser hide all
track name=regulatory description="TeleGene(tm) Regulatory Regions"
visibility=2
chr22  TeleGene	enhancer  10000000  10001000  500	+  .  TG1
chr22  TeleGene	promoter  10010000  10010100  900	+  .  TG1
chr22  TeleGene	promoter  10020000  10025000  800	-  .  TG2Click 
here to display this track in the Genome Browser. |  | 
 
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 | 
	
  	
  	
	
  	
  	| | |  | 
|---|
 |  | 
The datasets for the built-in microarray tracks in the Genome Browser are stored
in BED15 format, an extension of BED format that includes
three additional fields: expCount, expIds, and expScores. 
To display correctly in the Genome Browser, microarray tracks 
require the setting of several attributes in the trackDb file associated with 
the track's genome assembly. Each microarray track set must also have an 
associated microarrayGroups.ra configuration file that contains additional 
information about the data in each of the arrays. 
User-created microarray custom tracks are similar in format to BED 
custom tracks with the addition of three required track line parameters in the 
header--expNames, expScale, and expStep--that mimic the trackDb and 
microarrayGroups.ra settings of built-in microarray tracks.  
For a complete description of the microarray track format and an explanation
of how to construct a microarray custom track, see the 
Genome Browser Wiki.
 |  | 
 
 | 
 | 
	
  	
  	| | | 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). 
 
 Step 1.
Put your formatted annotation file on your web site. Be sure that 
the file permissions allow it to be read by others. Step 2.
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: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 %40, resulting in
the modified password mypwd%40wk.
 Combine the above pieces of information into a URL of the following
format (the information specific to your annotation file is highlighted):
 http://genome.ucsc.edu/cgi-bin/hgTracks?org=organism_name&
 position=chr_position&hgt.customText=URL.
 Example 10: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
http://genome.ucsc.edu/goldenPath/help/test.bed:
 
 http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr22&
 hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed
 
 
 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 
genome@soe.ucsc.edu. 
        
 Example 11: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:
bigBed, 
bigWig,
BAM, or
VCF.
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:
 
 http://genome.ucsc.edu/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
 
 
 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 
genome@soe.ucsc.edu 
        
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 
cut-and-paste operation
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'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
button.
 |  | 
 
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