Ucsc genome browser download custom track

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. 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.

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.

You may also use this interface to upload and manage custom track sets for multiple genome assemblies. Or, when browsing tracks, click the "add custom tracks" button below the Genome Browser. 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 Displaying and Managing Custom Tracks for more information. Load the custom track data 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:. Multiple custom tracks may be uploaded at one time on the Add Custom Tracks page through one of the following methods:.

NOTE: Please limit the number of custom tracks that you upload and maintain to less than tracks. If you have more than this suggested limit of tracks, please consider setting up a track hub instead. Optional Load the custom track description page 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:. 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.

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.

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. Displaying a custom track in the Genome Browser 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. Viewing a custom track in the Table Browser 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. 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.

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 "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. 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:. 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. You can also find instructions on how to find this table name in the video " How do I learn which tables belong to a data track on the UCSC Genome Browser?

To find the symbolic name of a composite track, look in the tableName field in the trackDb 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. 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 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.

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. Here is an example of a properly formatted track line using the bigBed format, with accompanying browser line:.

To make your Genome Browser annotation track viewable by people on other machines or at other sites, follow the steps below. Put your formatted annotation file on your web site. Be sure that the file permissions allow it to be read by others. The URL must contain 3 pieces of information specific to your annotation data:. 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.

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. 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.

This means that that link will show the Genome Browser default settings such as track selections, custom tracks, and track hubs. 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.

Any changes made to this window will not be saved and are lost as soon as the window is closed. To configure the display, set track and browser line attributes as described in the User's Guide. Examples are here. If you do not have web-accessible data storage available, please see the Hosting section of the Track Hub Help documentation. Please note a much more efficient way to load data is to use Track Hubs , which are loaded from the Track Hubs Portal found in the menu under My Data.

Loading Custom Tracks An annotation data file in one of the supported custom track formats may be uploaded by any of the following methods:. 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. 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 list. 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. 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 Browser lines configure the overall display of the Genome Browser window when your annotation file is uploaded. Each line defines one display attribute. 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. 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. Multiple track names should be space-separated. 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.

Symbolic names must be used. See NOTE for "dense all". 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 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. 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.

Step 1. Put your formatted annotation file on your web site. Be sure that the file permissions allow it to be read by others. 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. The genome position to which the Genome Browser should initially open. The URL of the annotation file on your web site. This information is of the form hgt. If a login and password is required to access data loaded through a URL e. Note that passwords included in URLs are not protected. Provide the URL to others. 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.

Example 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. 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. 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. Messages sent to this address will be posted to the moderated genome mailing list, which is archived on a public Web-accessible pipermail archive. 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. Loading a Custom Track into the Genome Browser. 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. Browser Lines. Browser lines configure the overall display of the Genome Browser window when your annotation file is uploaded.