Assembly Hubs: Difference between revisions
From genomewiki
Jump to navigationJump to search
(initial comments) |
(add example URL reference) |
||
| Line 23: | Line 23: | ||
http://yourLab.yourInstitution.edu/myHub/hub.txt | http://yourLab.yourInstitution.edu/myHub/hub.txt | ||
</nowiki> | </nowiki> | ||
You can view a working example hierarchy of files at: | |||
[http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/ Plants] | |||
==hub.txt== | |||
The initial file [http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/hub.txt hub.txt] is the primary URL reference for your assembly hub. | |||
Revision as of 21:49, 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. You will 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.
