Download bed file genome browser more than 100000 lines

The twoBitToFa command is available from the list of public utilities , in the directory appropriate to your operating system. Summary twoBitToFa and faCount are two useful utilities, among the many other hundreds of tools available, that are useful for extracting sequence data.

For almost 4 years, Genome Browser users have been able to use the Variant Annotation Integrator VAI to predict the functional effects of their variants of interest. The VAI is quite flexible, and offers the option to choose any gene set or gene prediction track in the chosen genome database for functional annotation.

Conservation scores may also be added to the output. To reduce the volume of output and narrow in on the variants that are most likely to damage genes, filters can be added to restrict the output to specific functional effects such as missense, frameshift, etc. Unfortunately, as a web tool the VAI does have some limitations, namely that only , variants at a time can be annotated, which prevents annotating variants derived from whole genome sequencing experiments.

Now our new vai. The script has many of the same configuration options as the web-based VAI, including filtering via functional effect term, position filters, and dbSNP rsID annotation. For example, say you have a VCF file with a couple thousand variants and you want to check to see if there are any dbSNP rs IDs associated with your variants.

Use the --rsId option:. What if your colleague gave you a list of rs IDs, and you want to know what genes they fall in and what changes they might cause? Just pass vai. What if you only care about the variants that fall on chr22? Well good thing vai. By default, vai. The following example compares the number of annotated variants with default settings and with the --variantLimit option Please note the grep command at the end is only a rough approximation of finding all the unique variants :.

Unfortunately the script will not annotate more than approximately 10,, variants due to the amount of memory needed it caps its usage at 6GB; this may change in the future , so setting the --variantLimit option any higher than 10,, will not work.

Instead you will need to split up your VCF file. For a full list of all the options outlined here as well as others, run vai. The script has some other drawbacks as well. This is because under the hood the script uses the existing web-based VAI executable to run, which in turn requires either manual compilation of our source code, or a precompiled binary from our downloads server.

Furthermore, VAI is tightly coupled to our genome databases and files. Secondly, users will need to have a. Our source tree includes a very minimal hg. GBiB users should have a functioning. This will take care of most of the work outside of fine-tuning a few settings like the udc.

For more information about hg. Any questions about fine-tuning these parameters should be sent to our public support forum mentioned below. If you encounter issues or have any questions while running vai. Choice of transcripts and software has a large effect on variant annotation. Genome Med. Track and assembly hubs are collections of data that are hosted on your servers and can be displayed using the UCSC Genome Browser and other genome browsers supporting the UCSC track hub format.

Track hubs allow for the visualization of data on assemblies that we already host such as the human or mouse genomes , while assembly hubs can be used to create genome browsers for any genome assembly of your choosing. Hubs depend on a number of different plain text configuration files. The most important are the trackDb. As the track hub format has grown in popularity, other genome browsers, including Ensembl , Biodalliance , and the WashU Epigenome Browser , have implemented support for the UCSC track hub format.

The Ensembl genome browser currently boasts fairly comprehensive support of the UCSC track hub format. In addition to supporting track hubs on their site, the Ensembl team has also created a Track Hub Registry that pulls hubs listed on our Public Hubs page into a centralized database alongside those hubs submitted to their registry. In an attempt to make the adoption of our track hub format easier, we talked to the other genome browsers about what settings were core to a track hub being, well, a track hub.

We sort the list of hundreds of settings into various support levels, which include:. We periodically increment the trackDb version number as major updates and changes are made to the settings. You can see more examples of how you might use hubCheck to check the compatibility of your hub with other genome browsers in our help documentation.

To acquire hubCheck, you can click Downloads from the top blue menu bar and then select Utilities and navigate to the utilities directory. If you have questions about creating or validating your track and assembly hubs, please feel free to contact us! Questions about other genome browsers support for hubs should be directed to their mailing lists.

It also contains tracks that break up the annotation set into a few subsets. All of the coordinates and alignments in these tracks are provided by the RefSeq group. This was a good solution in the past, but over time this method has led to some issues with transcripts matching to multiple places and our alignments of small exons or other regions differing slightly from those found in the RefSeq database.

First, as mentioned previously, the new tracks are based entirely on positions and alignments provided by RefSeq. Starting with the Apr. Because this sequence is not quite finished, it could not be included in the main "finished" ordered and oriented section of the chromosome. Also, in a very few cases in the Apr. There are a few clones in other chromosomes that also correspond to a different haplotype.

Because the primary reference sequence can only display a single haplotype, these alternatives were included in random files.

In subsequent assemblies, these regions have been moved into separate files e. ChrUn contains clone contigs that cannot be confidently placed on a specific chromosome. The coordinates of these are fairly arbitrary, although the relative positions of the coordinates are good within a contig. You can find more information about the data organization and format on the Data Organization and Format page.

There is a large block of N s at the beginning and end of chr Search for an A to bypass the initial group of N s. The following table shows the mapping of chromosomes in the chimp draft assemblies to human chromosomes. Starting with the panTro2 assembly, the numbering scheme was changed to reflect a new standard that preserves orthology with human chromosomes. Initially proposed by E. McConkey in , the new numbering convention was subsequently endorsed by the International Chimpanzee Sequencing and Analysis Consortium.

This standard assigns the identifiers "2a" and "2b" to the two chimp chromosomes that fused in the human genome to form chromosome 2 and renumbers the other chromosomes to more closely match their human counterparts. As a result, chromosomes 2 and 23 present in the panTro1 assembly do not exist in later versions.

You can migrate sequences from one assembly to another by using the Blat alignment tool or by converting assembly coordinates. There are two conversion tools available on the Genome Browser web site: the Convert utility and the LiftOver tool.

The Convert utility, which is accessed from the View menu on the Genome Browser annotation tracks page, supports forward, reverse, and cross-species conversions, but does not accept batch input.

The LiftOver tool, accessed via the Tools link on the Genome Browser home page, also supports forward, reverse, and cross-species conversions, as well as batch conversions. If you wish to update a large number of coordinates to a different assembly and have access to a Linux platform, you may find it useful to try the command-line version of the LiftOver tool.

The executable file for this utility can be downloaded here. LiftOver requires a pre-generated over. If the desired file is not available, send a request to the genome mailing list and we may be able to provide you with one. For the Known Genes, use the kgAlias table. To obtain a complete copy of the entire Known Genes data set for an organism, open the Genome Browser Downloads page , jump to the section specific to the organism, click the Annotation database link in that section, then click the link for the knownGene.

Set the position to the region of interest, then click the "get output" button. UCSC uses the latest versions of RepeatMasker and repeat libraries available on the date when the assembly data is processed.

Masking is done using the RepeatMasker -s flag. For mouse repeats, we also use -m. In addition to RepeatMasker, we use the Tandem Repeat Finder trf program, masking out repeats of period 12 or less.

The repeats are just "soft" masked. Alignments are allowed to extend through repeats, but not initiate in them. Yes, you can obtain the repeat-masked files via the Table Browser or from the organism's annotation database downloads directory. UCSC occasionally uses updated versions of the RepeatMasker software and repeat libraries that are not yet available on the RepeatMasker website see Repeat-masking data for more information.

The Genome Browser downloads site provides prepackaged downloads of bp, bp, and bp upstream sequence for RefSeq genes that have a coding portion and annotated 5' and 3' UTRs. You can obtain these from the bigZips downloads directory for the assembly of interest. To fetch the upstream sequence for a specific gene, use the Table Browser. Enter the genome, assembly, and select the knownGene table.

Paste the gene name or accession number in the identifier field. Choose sequence for the output format type, then click the get output button.

On the next page, select genomic. On the final page, you will have the opportunity to configure the amount of upstream promoter sequence to fetch, along with several other options. Click Get Sequence when you've finished configuring the output. Gene Sorter - expression, homology, and other information on groups of genes that can be related in many ways. To get started, click the Browser link on the blue sidebar.

This will take you to a Gateway page where you can select which genome to display. Note that there are also official mirror sites in Europe and Asia for users who are geographically closer to those continents than to the western United States.

To get oriented in using the Genome Browser, try viewing a gene or region of the genome with which you are already familiar, or use the default position.

To open the Genome Browser window:. Occasionally the Gateway page returns a list of several matches in response to a search, rather than immediately displaying the Genome Browser window. When this occurs, click on the item in which you're interested and the Genome Browser will open to that location. The search mechanism is not a site-wide search engine.

However, some types of queries will return an error, e. If your initial query is unsuccessful, try entering a different related term that may produce the same location. For example, if a query on a gene symbol produces no results, try entering an mRNA accession, gene ID number, or descriptive words associated with the gene.

If you have genomic, mRNA, or protein sequence, but don't know the name or the location to which it maps in the genome, the BLAT tool will rapidly locate the position by homology alignment, provided that the region has been sequenced.

This search will find close members of the gene family, as well as assembly duplication artifacts. An entire set of query sequences can be looked up simultaneously when provided in fasta format.

A successful BLAT search returns a list of one or more genome locations that match the input sequence.

To view one of the alignments in the Genome Browser, click the browser link for the match. The details link can be used to preview the alignment to determine if it is of sufficient match quality to merit viewing in the Genome Browser. You can open the Genome Browser window with a custom annotation track displayed by using the Add Custom Tracks feature available from the gateway and annotation tracks pages.

For more information on creating and using custom annotation tracks, refer to the Creating custom annotation tracks section. Once you've entered the annotation information, click the submit button at the top of the Gateway page to open up the Genome Browser with the annotation track displayed.

The Genome Browser also provides a collection of custom annotation tracks contributed by the UCSC Genome Bioinformatics group and the research community. NOTE: If an annotation track does not display correctly when you attempt to upload it, you may need to reset the Genome Browser to its default settings, then reload the track. For information on troubleshooting display problems with custom annotation tracks, refer to the troubleshooting section in the Creating custom annotation tracks section.

The Table Browser , a portal to the underlying open source MariaDB relational database driving the Genome Browser, displays genomic data as columns of text rather than as graphical tracks. For more information on using the Table Browser, see the section Getting started: on the Table Browser. Several external gateways provide direct links into the Genome Browser.

Journal articles can also link to the browser and provide custom tracks. Be sure to use the assembly date appropriate to the provided coordinates when using data from a journal source. To facilitate your return to regions of interest within the Genome Browser, save the coordinate range or bookmark the page of displays that you plan to revisit or wish to share with others.

It is usually best to work with the most recent assembly even though a full set of tracks might not yet be ready. Be aware that the coordinates of a given feature on an unfinished chromosome may change from one assembly to the next as gaps are filled, artifactual duplications are reduced, and strand orientations are corrected. The Genome Browser offers multiple tools that can correctly convert coordinates between different assembly releases.

For more information on conversion tools, see the section Converting data between assemblies. To ensure uninterrupted browser services for your research during UCSC server maintenance and power outages, bookmark a mirror site that replicates the UCSC genome browser.

Bear in mind that the Genome Browser cannot outperform the underlying quality of the draft genome. Assembly errors and sequence gaps may still occur well into the sequencing process due to regions that are intrinsically difficult to sequence. Artifactual duplications arise as unavoidable compromises during a build, causing misleading matches in genome coordinates found by alignment. The Genome Browser annotation tracks page displays a genome location specified through a Gateway search, a BLAT search, or an uploaded custom annotation track.

There are five main features on this page: a set of navigation controls , a chromosome ideogram, the annotations tracks image, display configuration buttons , and a set of track display controls.

The first time you open the Genome Browser, it will use the application default values to configure the annotation tracks display. By manipulating the navigation, configuration and display controls, you can customize the annotation tracks display to suit your needs. For a complete description of the annotation tracks available in all assembly versions supported by the Genome Browser, see the Annotation Track Descriptions section. The Genome Browser retains user preferences from session to session within the same web browser, although it never monitors or records user activities or submitted data.

To restore the default settings, click the "Click here to reset" link on the Genome Browser Gateway page. To return the display to the default set of tracks but retain custom tracks and other configured Genome Browser settings , click the default tracks button on the Genome Browser page.

Annotation track descriptions: Each annotation track has an associated description page that contains a discussion of the track, the methods used to create the annotation, the data sources and credits for the track, and in some cases filter and configuration options to fine-tune the information displayed in the track. To view the description page, click on the mini-button to the left of a displayed track or on the label for the track in the Track Controls section.

Annotation track details pages: When an annotation track is displayed in full, pack, or squish mode, each line item within the track has an associated details page that can be displayed by clicking on the item or its label. The information contained in the details page varies by annotation track, but may include basic position information about the item, related links to outside sites and databases, links to genomic alignments, or links to corresponding mRNA, genomic, and protein sequences.

Gene prediction tracks: Coding exons are represented by blocks connected by horizontal lines representing introns. The 5' and 3' untranslated regions UTRs are displayed as thinner blocks on the leading and trailing ends of the aligning regions. In full display mode, arrowheads on the connecting intron lines indicate the direction of transcription.

In situations where no intron is visible e. In dense display mode, the degree of darkness corresponds to the number of features aligning to the region or the degree of quality of the match. In pack or full display mode, the aligning regions are connected by lines representing gaps in the alignment typically spliced-out introns , with arrowheads indicating the orientation of the alignment, pointing right if the query sequence was aligned to the forward strand of the genome and left if aligned to the reverse strand.

Two parallel lines are drawn over double-sided alignment gaps, which skip over unalignable sequence in both target and query. For alignments of ESTs, the arrows may be reversed to show the apparent direction of transcription deduced from splice junction sequences. In situations where no gap lines are visible, the arrowheads are displayed on the block itself.

To prevent display problems, the Genome Browser imposes an upper limit on the number of alignments that can be viewed simultaneously within the tracks image. When this limit is exceeded, the Browser displays the best several hundred alignments in a condensed display mode, then lists the number of undisplayed alignments in the last row of the track. In this situation, try zooming in to display more entries or to return the track to full display mode.

For some PSL tracks, extra coloring to indicate mismatching bases and query-only gaps may be available. Chain tracks 2-species alignment : Chain tracks display boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the genome of the first species or an insertion in the genome of the second species.

Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where there are multiple chains over a particular portion of the genome, chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.

In the fuller display modes, the individual feature names indicate the chromosome, strand, and location in thousands of the match for each matching alignment.

Net tracks 2-species alignment : Boxes represent ungapped alignments, while lines represent gaps. Clicking on a box displays detailed information about the chain as a whole, while clicking on a line shows information on the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types other than gap :.

Snake tracks: The snake alignment track or snake track shows the relationship between the chosen Browser genome reference genome and another genome query genome. A snake is a way of viewing a set of pairwise gapless alignments that may overlap on both the reference and query genomes.

Alignments are always represented as being on the positive strand of the reference species, but can be on either strand on the query sequence. In full display mode, a snake track can be decomposed into two drawing elements: segments colored rectangles and adjacencies lines connecting the segments.

Segments represent subsequences of the target genome aligned to the given portion of the reference genome. Adjacencies represent the covalent bonds between the aligned subsequences of the target genome. Red tick-marks within segments represent substitutions with respect to the reference, shown in windows of the reference of by default up to 50 Kb.

Zoomed in to the base level, these substitutions are labeled with the non-reference base. An insertion in the reference relative to the query creates a gap between abutting segment sides that is connected by an adjacency. An insertion in the query relative to the reference is represented by an orange tick-mark that splits a segment at the location the extra bases would be inserted.

Simultaneous independent insertions in both query and reference look like an insertion in the reference relative to the target, except that the corresponding adjacency connecting the two segments is colored orange. More complex structural rearrangements create adjacencies that connect the sides of non-abutting segments in a natural fashion.

Pack mode can be used to display a larger number of snake tracks in the limited vertical browser. This mode eliminates the adjacencies from the display and forces the segments onto as few rows as possible, given the constraint of still showing duplications in the query sequence. Dense mode further eliminates these duplications so that each snake track is compactly represented along just one row.

Wiggle tracks: These tracks plot a continuous function along a chromosome. Data is displayed in windows of a set number of base pairs in width. The score for each window displays as "mountain ranges" The display characteristics vary among the tracks in this group.

See the individual track descriptions for more information on interpreting the display. If the peak is taller or shorter than what can be shown in the display, it is clipped and colored magenta. Each annotation track within the window may have up to five display modes: Hide: the track is not displayed at all. To hide all the annotation tracks, click the hide all button. This mode is useful for restricting the display to only those tracks in which you are interested.

For example, someone who is not interested in SNPs or mouse synteny may want to hide these tracks to reduce track clutter and improve speed.

There are a few annotation tracks that pertain only to one specific chromosome, e. Sanger22, Rosetta. In these cases, the track and its associated controller will be hidden automatically when the track window is not open to the relevant chromosome.

Dense: the track is displayed with all features collapsed into a single line. This mode is useful for reducing the amount of space used by a track when you don't need individual line item details or when you just want to get an overall view of an annotation.

For example, by opening an entire chromosome and setting the RefSeq Genes track to dense, you can get a feel for the known gene density of the chromosome without displaying excessive detail.

Full: the track is displayed with each annotation feature on a separate line. It is recommended that you use this option sparingly, due to the large number of individual track items that may potentially align at the selected position. For example, hundreds of ESTs might align with a specified gene. When the number of lines within a requested track location exceeds , the track automatically defaults to a more tightly-packed display mode.

In this situation, you can restore the track display to full mode by narrowing the chromosomal range displayed or by using a track filter to reduce the number of items displayed. On tracks that contain only hide, dense, and full modes, you can toggle between full and dense display modes by clicking on the track's center label.

Features are unlabeled, and more than one may be drawn on the same line. This mode is useful for reducing the amount of space used by a track when you want to view a large number of individual features and get an overall view of an annotation.

It is particularly good for displaying tracks in which a large number of features align to a particular section of a chromosome, e. EST tracks. Pack: the track is displayed with each annotation feature shown separately and labeled, but not necessarily displayed on a separate line.

This mode is useful for reducing the amount of space used by a track when you want to view the large number of individual features allowed by squish mode, but need the labeling and display size provided by full mode. When the number of lines within the requested track location exceeds , the track automatically defaults to squish display mode. In this situation, you can restore the track display to pack mode by narrowing the chromosomal range displayed or by using a track filter to reduce the number of items displayed.

To toggle between pack and full display modes, click on the track's center label. The track display controls are grouped into categories that reflect the type of data in the track, e. To change the display mode for a track, find the track's controller in the Track Controls section at the bottom of the Genome Browser page, select the desired mode from the control's display menu, and then click the refresh button. Alternatively, you can change the display mode by using the Genome Browser's right-click navigation feature, or can toggle between dense and full modes for a displayed track or pack mode when available by clicking on the optional center label for the track.

Track display modes may be set individually or as a group on the Genome Browser Track Configuration page. To access the configuration page, click the configure button on the annotation tracks page or the configure tracks and display button on the Gateway page.

Exercise caution when using the show all buttons on track groups or assemblies that contain a large number tracks; this may seriously impact the display performance of the Genome Browser or cause your Internet browser to time out.

The entire set of track display controls at the bottom of the annotation tracks page may be hidden from view by checking the Show track controls under main graphic option in the Configure Image section of the Track Configuration page. Some tracks have additional filter and configuration capabilities, e. These options let the user modify the color or restrict the data displayed within an annotation track. Filters are useful for focusing attention on items relevant to the current task in tracks that contain large amounts of data.

For example, to highlight ESTs expressed in the liver, set the EST track filter to display items in a different color when the associated tissue keyword is "liver" Configuration options let the user adjust the display to best show the data of interest.

For example, the min vertical viewing range value on wiggle tracks can be used to establish a data threshold. By setting the min value to "50", only data values greater than 50 percent will display.

To access filter and configuration options for a specific annotation track, open the track's description page by clicking the label for the track's control menu under the Track Controls section, the mini-button to the left of the displayed track, or the "Configure The filter and configration section is located at the top of the description page.

In most instances, more information about the configuration options is available within the description text or through a special help link located in the configuration section. Filter and configuration settings are persistent from session to session on the same web browser. To return the Genome Browser display to the default set of tracks but retain custom tracks and other configured Genome Browser settings , click the default tracks button on the Genome Browser tracks page.

To remove all user configuration settings and custom tracks, and completely restore the defaults, click the "Click here to reset" link on the Genome Browser Gateway page. At times you may want to adjust the amount of flanking region displayed in the annotation tracks window or adjust the scale of the display. At a scale of 1 pixel per base pair, the window accurately displays the width of exons and introns, and indicates the direction of transcription using arrowheads for multi-exon features.

At a grosser scale, certain features - such as thin exons - may disappear. Also, some exons may falsely appear to fall within RepeatMasker features at some scales. Consequently, we have developed the following two programs, both of which are available from the directory of binary utilities.

As with all UCSC Genome Browser programs, simply type the program name at the command line with no parameters to see the usage statement. If you get an error when you run the bedToBigBed program, it may be because your input BED file has data off the end of a chromosome. In this case, use the bedClip program here before the bedToBigBed program. It will remove the row s in your input BED file that are off the end of a chromosome. Example Two In this example, you will create your own bigBed file from an existing bed file.

Save this. This is required when the BED file contains a field for color. Because this bigBed file includes a field for color, you must include the itemRgb attribute in the "track" line. Note that the original BED file contains data only on chromsome 7. Extracting Data from the bigBed Format Because the bigBed files are indexed binary files, they can be difficult to extract data from.

Troubleshooting If you get an error when you run the bedToBigBed program, it may be because your input BED file has data off the end of a chromosome.