How to download snp from ucsc genome browser

The tables in this section contain additional information about mRNA sequences. JavaScript is disabled in your web browser You must have JavaScript enabled in your web browser to use the Genome Browser.

The Genome Browser Database. Table Descriptions. Tables Split by Chromosome. Data Stored in a Single Table. The tables in this section contain data stored in a single table rather than in one table per chromosome. See Lo Conte, Brenner et al.

Internal Use Tables. The tables in this section are intended primarily for internal use. 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. 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.

These links also display under a column titled "UCSC version" on the conservation track description page. Some files in the browser, such as bigBed files, are hosted in binary format. For example, in the hg38 database, the crispr. The bigBedToBed tool can also be used to obtain a specific subset of features within a given range, e. Data on the gbdb fileserver can also be acquired using the rsync commands outline on our FTP downloads page.

This technique is especially useful for downloading large files. For example, the link for the mm5-to-mm6 over. The link to download the liftOver source is located in the Source and utilities downloads section. JavaScript is disabled in your web browser You must have JavaScript enabled in your web browser to use the Genome Browser.

Denisova S. Access source using git Download source code. Multiple alignments of 99 vertebrate genomes with human Conservation scores for alignments of 99 vertebrate genomes with human Basewise conservation scores phyloP of 99 vertebrate genomes with human FASTA alignments of 99 vertebrate genomes with human for CDS regions Multiple alignments of 45 vertebrate genomes with human Conservation scores for alignments of 45 vertebrate genomes with human Basewise conservation scores phyloP of 45 vertebrate genomes with human FASTA alignments of 45 vertebrate genomes with human for CDS regions.

Multiple alignments of 43 vertebrate genomes with human Conservation scores for alignments of 43 vertebrate genomes with human Basewise conservation scores phyloP of 43 vertebrate genomes with human FASTA alignments of 43 vertebrate genomes with human for CDS regions Multiple alignments of 27 vertebrate genomes with human Conservation scores for alignments of 27 vertebrate genomes with human Basewise conservation scores phyloP of 27 vertebrate genomes with human FASTA alignments of 27 vertebrate genomes with human for CDS regions Multiple alignments of 16 vertebrate genomes with human Conservation scores for alignments of 16 vertebrate genomes with human Multiple alignments of 35 vertebrate genomes with human in ENCODE regions.

Multiple alignments of 16 vertebrate genomes with Human Conservation scores for alignments of 16 vertebrate genomes with Human Multiple alignments of 8 vertebrate genomes with Human Conservation scores for alignments of 8 vertebrate genomes with Human.

Multiple alignments of 3 vertebrate genomes with Cat Conservation scores for alignments of 3 vertebrate genomes with Cat. Multiple alignments of 77 vertebrate genomes with Chicken Conservation scores for alignments of 77 vertebrate genomes with Chicken Basewise conservation scores phyloP of 77 vertebrate genomes with Chicken. Multiple alignments of 6 vertebrate genomes with chicken Conservation scores for alignments of 6 vertebrate genomes with chicken. Multiple alignments of 4 vertebrate genomes with Cow Conservation scores for alignments of 4 vertebrate genomes with Cow.

Multiple alignments of 3 vertebrate genomes with Dog Conservation scores for alignments of 3 vertebrate genomes with Dog. Multiple alignments of 7 vertebrate genomes with Fugu Conservation scores for alignments of 7 vertebrate genomes with Fugu. Multiple alignments of 4 vertebrate genomes with Fugu Conservation scores for alignments of 4 vertebrate genomes with Fugu.

You may want to use the prompt command to toggle the interactive mode if you do not want to be prompted for each file that you download. JavaScript is disabled in your web browser You must have JavaScript enabled in your web browser to use the Genome Browser. Downloading data Rsync recommended method We recommend that you download data via rsync using the command line, especially for large files using the North American or European download servers.