Assembly Hubs: Difference between revisions
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at this hub. Typically '''genomes.txt''' is at the same directory level as this '''hub.txt''', however it can also be a relative path | at this hub. Typically '''genomes.txt''' is at the same directory level as this '''hub.txt''', however it can also be a relative path | ||
reference to a different directory level. | reference to a different directory level. | ||
The ''email'' address provides users a contact point for queries related to this assembly hub. | |||
==genomes.txt== | ==genomes.txt== | ||
The [http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/genomes.txt genomes.txt] file provides the references to the | The [http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/genomes.txt genomes.txt] file provides the references to the | ||
genome assemblies and tracks available at this assembly hub. | genome assemblies and tracks available at this assembly hub. | ||
Revision as of 22:08, 17 April 2013
Overview
The Assembly Hub function is new technology in the UCSC Genome Browser as of early 2013 which allows you to display your novel genome sequence using the UCSC Genome Browser
Web Server
To display your novel genome sequence, you use a web server at your institution to supply your files to the UCSC Genome Browser. Establish a hierarchy of directories and files to host your novel genome sequence. For example:
myHub/ - directory to organize your files on this hub
hub.txt – primary reference text file to define the hub, refers to:
genomes.txt – definitions for each genome assembly on this hub
newOrg1/ - directory of files for this specific genome assembly
newOrg1.2bit – ‘2bit’ file constructed from your fasta sequence
description.html – information about this assembly for users
trackDb.txt – definitions for tracks on this genome assembly
groups.txt – definitions for track groups on this assembly
bigWig and bigBed files – data for tracks on this assembly
external track hub data tracks can be displayed on this assembly
The URL to reference this hub would be: http://yourLab.yourInstitution.edu/myHub/hub.txt
You can view a working example hierarchy of files at: Plants
hub.txt
The initial file hub.txt is the primary URL reference for your assembly hub. The format of the file:
hub hubName shortLabel genome longLabel Comment describing this hub contents genomesFile genomes.txt email contactEmail@institution.edu
The shortLabel is the name that will appear in the genome pull-down menu at the UCSC gateway page. Example: Plants
The genomesFile is a reference to the next definition file in this chain that will describe the assemblies and tracks available at this hub. Typically genomes.txt is at the same directory level as this hub.txt, however it can also be a relative path reference to a different directory level.
The email address provides users a contact point for queries related to this assembly hub.
genomes.txt
The genomes.txt file provides the references to the genome assemblies and tracks available at this assembly hub.
