Downloadable txt coordinate files

To get an overview of the interface, you can watch this introduction video. Since the project started by the end of the 's, our server has registered more than 31, accounts. See our reference page for a list of published studies featuring Brainstorm at work. The best way to learn how to use Brainstorm, like any other academic software, is to benefit from local experts.

You currently have javascript disabled. Several functions may not work. Please re-enable javascript to access full functionality. Community Forum Software by IP. Board Licensed to: VPForums. Sign In Create Account. Javascript Disabled Detected You currently have javascript disabled. Schuss Rally 1. Seven Winner Inder 1. Five nights at freddy FNAF 1.

Top Authors Past Month. It was co built by myself 85vett an Who Framed Roger Rabbi Disney The Little Merm The deadline for the file request. Deadlines can only be set by Professional and Business accounts. If set, allow uploads after the deadline has passed.

These uploads will be marked overdue. GracePeriod open union. If the file request is closed, it will not accept any file submissions, but it can be opened later. The default for this field is True. A description of the file request. If the file request is closed, it will not accept any more file submissions. The path of the folder in the Dropbox where uploaded files will be sent. This can be None if the destination was removed. The deadline for this file request. Only set if the request has a deadline.

Apps with the app folder permission can only access file requests in their app folder. File requests are only available on accounts with a verified email address.

Users can verify their email address here. For example, the title was invalid, or there were disallowed characters in the destination path. The limit is currently file requests total. Apps with the app folder permission will only see file requests in their app folder. The default for this field is ListFileRequestsContinueError union.

The new title of the file request. The new path of the folder in the Dropbox where uploaded files will be sent. UpdateFileRequestDeadline open union. If None, the file request's deadline is cleared. Whether to set this file request as open or closed. The description of the file request. This flag has no effect. The default for this field is False. This does not apply to copies. This never contains a slash. Since this time is not verified the Dropbox server stores whatever the desktop client sends up , this should only be used for display purposes such as sorting and not, for example, to determine if a file has changed or not.

This field is the same rev as elsewhere in the API and can be used to detect changes and avoid conflicts. The lowercased full path in the user's Dropbox. This always starts with a slash. This field will be null if the file or folder is not mounted. The cased path to be used for display purposes only. In rare instances the casing will not correctly match the user's filesystem, but this behavior will match the path provided in the Core API v1, and at least the last path component will have the correct casing.

Field is deprecated. Please use FileSharingInfo. Additional information if the file is a photo or video. MediaInfo union. MediaMetadata datatype with subtypes. The duration of the video in milliseconds. Set if this file is a symlink. Set if this file is contained in a shared folder. The last user who modified the file. This field will be null if the user's account has been deleted. Information about format this file can be exported to. Format to which the file can be exported to.

Additional formats to which the file can be exported. Additional information if the file has custom properties with the property template specified. If this flag is present, it will be true if this file has any explicit shared members.

A hash of the file content. This field can be used to verify data integrity. For more information see our Content hash page. If present, the metadata associated with the file's current lock. True if caller holds the file lock. The display name of the lock holder. The account ID of the lock holder if known. The timestamp of the lock was created. Set if the folder is contained in a shared folder or is a shared folder mount point.

Set if the folder is contained by a shared folder. If this folder is a shared folder mount point, the ID of the shared folder mounted at this location. They do, however, have access to some sub folder.

Note that only properties associated with user-owned templates, not team-owned templates, can be attached to folders. The given path does not satisfy the required path format. Please refer to the Path formats documentation for more information. WriteConflictError open union. Please retry this request. This is not allowed.

You may reissue the request with the field RelocationArg. You'll need to verify that the action you were taking succeeded, and if not, try again. This should happen very rarely. MoveIntoVaultError open union. Metadata datatype with subtypes. Each entry is RelocationPath. The string is an id that can be used to obtain the status of the asynchronous job. RelocationBatchResultEntry open union. RelocationError open union. This is the value of a response returned from the method that launched the job.

RelocationBatchError union. This value is currently set to be far enough in the future so that expiration is effectively not an issue. Please make sure this app is same app which created the copy reference and the source user is still linked to the app.

Duplicate path arguments in the batch are considered only once. CreateFolderBatchResultEntry union. CreateFolderBatchJobStatus open union. CreateFolderBatchError open union. Perform delete if given "rev" matches the existing file's latest "rev". This field does not support deleting a folder.

Please retry with fewer files. DeleteBatchResultEntry union. DeleteBatchError open union. Use DeleteError. Please specify revision in path instead. The file format to which the file should be exported. A hash based on the exported file content. Similar to content hash. Use download instead. Please retry later. Each 'entry' contains a path of the file which will be locked or queried. LockFileResultEntry union. The file lock state after the operation. FileLockContent open union.

The id of the team of the account holder if it exists. LookupError open union. If set to a valid list of template IDs, FileMetadata. TemplateFilterBase open union. This functionality is only available on accounts with a verified email address.

This size varies among images. The image may be zoomed in or out, sized to match the resolution of the original image or best fit the image display window, and moved or scrolled in any direction to focus on areas of interest. The original full-sized image may also be downloaded. Zooming in: To enlarge the image by 2X, click the Zoom in button above the image or click on the image using the left mouse button. Zooming out: To reduce the image by 2X, click the Zoom out button above the image or click on the image using the right mouse button.

Alternatively, the - key may be used to zoom out when the main image pane is the active window. Sizing to full resolution: Click the Zoom full button above the image to resize the image such that each pixel on the screen corresponds to a pixel in the digitized image. Sizing to best fit: Click the Zoom fit button above the image to zoom the image to the size that best fits the main image pane.

Moving the image: To move the image viewing area in any direction, click and drag the image using the mouse. Alternatively, the following keyboard shortcuts may be used after clicking on the image: Scroll left in the image: Left-arrow key or Home key Scroll right in the image: Right-arrow key or End key Scroll up in the image: Up-arrow key or PgUp key Scroll down in the image: Down-arrow key or PgDn key Downloading the original full-sized image: Most images may be viewed in their original full-sized format by clicking the "download" link at the bottom of the image caption.

NOTE: due to the large size of some images, this action may take a long time and could potentially exceed the capabilities of some Internet browsers. If you have an image set you would like to contribute for display in the VisiGene Browser, contact Jim Kent. The Genome Browser provides a feature to configure the retrieval, formatting, and coloring of the text used to depict the DNA sequence underlying the features in the displayed annotation tracks window.

Retrieval options allow the user to add a padding of extra bases to the upstream or downstream end of the sequence. Formatting options range from simply displaying exons in upper case to elaborately marking up a sequence according to multiple track data.

The DNA sequence covered by various tracks can be highlighted by case, underlining, bold or italic fonts, and color. The DNA display configuration feature can be useful to highlight features within a genomic sequence, point out overlaps between two types of features for example, known genes vs.

To display extra bases upstream of the 5' end of your sequence or downstream of the 3' end of the sequence, enter the number of bases in the corresponding text box. This option is useful in looking for regulatory regions. The Sequence Formatting section lists several options for adjusting the case of all or part of the DNA sequence.

To choose one of these formats, click the corresponding option button, then click the get DNA button. The page provides instructions for using the formatting table, as well as examples of its use.

The list of tracks in the Track Name column is automatically generated from the list of tracks available on the current genome. Keep the formatting simple at first: it is easy to make a display that is pretty to look at but is also completely cryptic. Also, be careful when requesting complex formatting for a large chromosomal region: when all the HTML tags have been added to the output page, the file size may exceed the size limits that your Internet browser, clipboard, and other software can safely display.

The maximum size of genome that can be formatted by the tool is approximately 10 Mbp. Coordinates of features frequently change from one assembly to the next as gaps are closed, strand orientations are corrected, and duplications are reduced.

Occasionally, a chunk of sequence may be moved to an entirely different chromosome as the map is refined. There are three different methods available for migrating data from one assembly to another: BLAT alignment, coordinate conversion, and coordinate lifting. The Genome Browser Convert utility is useful for locating the position of a feature of interest in a different release of the same genome or in some cases in a genome assembly of another species.

During the conversion process, portions of the genome in the coordinate range of the original assembly are aligned to the new assembly while preserving their order and orientation. In general, it is easier to achieve successful conversions with shorter sequences.

When coordinate conversion is available for an assembly, click on the "View" pulldown on the top blue menu bar on the Genome Browser page and select the "In Other Genomes Convert " link.

Select the genome and assembly to which you'd like to convert the coordinates, then click the Submit button. If the conversion is successful, the browser will return a list of regions in the new assembly, along with the percent of bases and span covered by that region.

Click on a region to display it in the browser. If the conversion is unsuccessful, the utility returns a failure message. The liftOver tool is useful if you wish to convert a large number of coordinate ranges between assemblies. You can use the BED format e. See our Coordinate Counting blog post for a discussion of the difference.

If the coordinates do not cover a single base pair e. To access the graphical version of the liftOver tool, click on "Tools" pulldown in the top blue menu bar of the Genome Browser, then select LiftOver from the menu. Alternatively, you may load the coordinate ranges from an existing data file by entering the file name in the upload box at the bottom of the screen, then clicking the Submit File button. The default parameter settings are recommended for general purpose use of the liftOver tool.

However, you may want to customize settings if you have several very large regions to convert. Command-line coordinate lifting The command-line version of liftOver offers the increased flexibility and performance gained by running the tool on your local server. This utility requires access to a Linux platform.

The executable file may be downloaded here. Pre-generated files for a given assembly can be accessed from the assembly's "LiftOver files" link on the Downloads page. If the desired conversion file is not listed, send a request to the genome mailing list and we may be able to generate one for you.

Most of the underlying tables containing the genomic sequence and annotation data displayed in the Genome Browser can be downloaded. This data was contributed by many researchers, as listed on the Genome Browser Credits page. Please acknowledge the contributor s of the data you use. Downloading the data Genome data can be downloaded in different ways using our North American and European download servers, hgdownload, hgdownload2, and hgdownload-euro.

There may be several download directories associated with each version of a genome assembly: the full data set bigZips , the full data set by chromosome chromosome , the annotation database tables database , and one or more sets of comparative cross-species alignments. Depending on the genome, this directory may contain some or all of the following files:. Chromosomes contains the assembled sequence for the genome in separate files for each chromosome in a zipped fasta format.

The main assembly can be found in the chrN. Database contains all of the positional and non-positional tables in the genome annotation database. Each table is represented by 2 files:. Schema descriptions for all tables in the genome annotation database may be viewed by using the "describe table schema" button in the Table Browser.

Cross-species alignments directories, such as the vsMm4 and humorMm3Rn3 directories in the hg16 assembly, contain pairwise and multiple species alignments and filtered alignment files used to produce cross-species annotations.

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. For a more stable option for custom annotations, we suggest using track hubs. A third, more technical, option is to operate a mirror. Custom tracks work well for quickly displaying data, while track hubs are more configurable and permanent.

Custom tracks are a wonderful tool for research scientists using the Genome Browser. Because space is limited in the Genome Browser track window, many excellent genome-wide tracks cannot be included in the standard set of tracks packaged with the browser.

Other tracks of interest may be excluded from distribution because the annotation track data is too specific to be of general interest or can't be shared until journal publication. In the past, many individuals and labs contributed custom tracks to the Genome Browser website for use by others.

To view a list of these custom annotation tracks, click here. Track hubs are now the preferred approach for viewing and sharing data on the Browser.

Labs, consortia, and institutions submit their hubs to be listed as a Public Hub. Track hubs require remotely hosted data. They use binary index files which allow the browser to quickly access only what is relevant for the current region being viewed in the browser.

See the track hub help page for more information. 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. Step 1. Format the data set: Format your data as a tab-separated file using one of the formats supported by the Genome Browser. 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. 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 bases on chr The second track displays red base features alternating with blank space in the same region of chr Example 3a: 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,,0 , and the gray level of the each feature reflects the score value of that line. Example 3b: This example shows a simple annotation file containing one data set in the bigBed format. This track displays random sized blocks across chr21 in the human genome. The big data formats, such as the bigBed format, can be uploaded using a bigDataUrl that is specified in the track line.

For more information on these track line parameters, refer to the Track Lines section. When using bigDataUrls, data is cached and updated every seconds. You may paste these two lines directly into the "Add Custom Tracks" page to view this example in the browser:. This will infer the track type as "bigBed" based on the file extension and set the track name to "bigBedExample".

Step 4. Display your annotation track in the Genome Browser From the Gateway page , select the genome assembly on which your annotation data is based, click 'GO', then click the "add custom tracks" or "manage custom tracks" button below the tracks window. 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. 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.