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 @@ -994,31 +994,31 @@
@@ -1366,87 +1366,87 @@
The command-line version of liftOver offers the increased flexibility and performance gained by running the tool on your local server. See an example of running the liftOver tool on the command line. This utility requires access to a Linux platform. The executable file may be downloaded here. Command-line liftOver requires a UCSC-generated over.chain file as input. Pre-generated files for a given assembly can be accessed from the assembly's "LiftOver files" link on -the Downloads page. If the desired +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. For use of the command-line version of LiftOver, we require all for-profit businesses or commercial companies to purchase a license to support our small team.
Most of the underlying tables containing the genomic sequence and annotation data displayed in the Genome Browser can be downloaded. All of the tables are freely usable for any purpose except as indicated in the README.txt file in the download directories. 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.
Genome data can be downloaded in different ways using our North American and European download servers, hgdownload, hgdownload2, and hgdownload-euro.
rsync -a -P rsync://hgdownload.soe.ucsc.edu/path/file ./rsync -a -P rsync://hgdownload.gi.ucsc.edu/path/file ./rsync -a -P rsync://hgdownload2.soe.ucsc.edu/path/file ./rsync -a -P rsync://hgdownload-euro.soe.ucsc.edu/path/file ./rsync -a -P rsync://hgdownload.soe.ucsc.edu/directory/ ./rsync -a -P rsync://hgdownload.gi.ucsc.edu/directory/ ./rsync -a -P rsync://hgdownload2.soe.ucsc.edu/directory/ ./rsync -a -P rsync://hgdownload-euro.soe.ucsc.edu/directory/ ./ftp://hgdownload.soe.ucsc.edu/goldenPath/,
+ ftp://hgdownload.gi.ucsc.edu/goldenPath/,
ftp://hgdownload2.soe.ucsc.edu/goldenPath/,
or
ftp://hgdownload-euro.soe.ucsc.edu/goldenPath/
will take you to a directory that contains the genome download directories. This download method
is not recommended if you plan to download a large file or multiple files from a single
directory compared to rsync (see above). You can, however, use the mget command to
download multiple files: mget filename1 filename2, or mget -a
(to download all the files in the directory).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.
BigZips contains the entire draft of the genome in chromosome and/or contig form. Depending on the genome, this directory may contain some or all of the following files:
@@ -1545,66 +1545,66 @@Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser alongside native annotation tracks. Hubs are a useful tool for visualizing a large number of genome-wide data sets. The Track Hub utility allows efficient access to data sets from around the world through the familiar Genome Browser interface. Browser users can display tracks from any public track hub that has been registered with UCSC. We offer guidelines for those who want to make a hub a public track hub. Additionally, users can import data from unlisted hubs or can set up, display, and share their own track hubs.
For information on using the Track Hub features, refer to the Genome Browser Track Hub User Guide. For specific information on configuring your trackDb.txt file, refer to the Track Database Definition Document. See also the Basic Hub Quick Start Guide, Quick Start Guide to Organizing Track Hubs into -Groupings, , Track hub settings blog post, Quick Start Guide to Assembly Hubs, Quick Start Guide to Searchable Track Hubs, and Loading Track Hubs and Assembly Hubs with the URL.
To construct a track hub that will display on a -GenArk Assembly hub, specify the GenArk assembly name in the genome statement in your hub.txt file as described below. For example, a reference such as:
genome GCA_021951015.1
will direct your track hub to display on the human Feb. 2022 - GCA_021951015.1 - HG002.mat.cur.20211005 genome assembly.
To share your track hub with your audience of interest, when you publish the URL to your track hub, that genome reference in your track hub.txt file will cause that associated assembly hub to display in the genome browser with your track hub annotations on that genome browser. There is no need to otherwise reference the assembly hub, it will automatically attach itself.
A complete list of all available GenArk assemblies available can be seen in the text file -UCSC_GI.assemblyHubList.txt.
Historically, a hub needed a set of text files to specify properties for a track hub and each of the data tracks within the hub. The track hub settings were stored in a three file structure: hub.txt, genomes.txt, and trackDb.txt
myHub/ - directory containing track hub files * hub.txt - a short description of hub properties * genomes.txt - list of genome assemblies included in the hub data * hg19/ - directory of data for the hg19 (GRCh37) human assembly ** trackDb.txt - display properties for tracks in this directory