Upload your data - URL
Introduction
Display your own data in Ensembl using a file with a url address. The data can be seen in 'ContigView' and 'CytoView' displays. Use the 'DAS' roll-down menu in these pages to get started.
This system is based on the custom annotation track system of the UCSC Genome Browser and details about the data formats can be found at: http://genome.ucsc.edu/goldenPath/help/customTrack.html
To add your web-based track to Ensembl, you need to:
- Format the data set
- Define information about the track
- Choose your window of the genome (Location line)
- Display in Ensembl
You may also find the following useful:
Formatting the Data Set
Firstly format your data as tab or space separated file using one of the following formats:
- GFF
- GTF
- BED
- PSL
- (new!) WIG
Details of some of these formats can be found at http://genome.ucsc.edu/goldenPath/help/customTrack.html
Notes:
-
You may include information for multiple tracks in the same file
-
As entries in GFF/GTF files may contain spaces, then columns in GFF/GTF files MUST be separated by a tab or at least 2 spaces.
Wiggle plots can be viewed for WIG and BED URL-based data.
BED FORMAT:
To display data in BED file as a colour gradient, histogram, tiling array or a wiggle plot you need to add 'useScore=X' to the track description ( http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK )
e.g
track name="Histogram" description="Histogram demonstration" visibility=2 useScore=X height=30
where X can be
1 - tiling array
2 - colourgradient
in case of colourgradient you can specify which colours to use to build gradient (cgColour1, cgColour2, cgColour3) and how many colour grades to use (cgGrades)
( these are the Ensembl extension and are optional parameters - by default Ensembl will create 20 shades of our standard colourgradient - Yellow-Green-Blue )
for example:
track name="ColorGradient" description="ColourGradient demonstration" visibility=2 useScore=2 cgGrades=50 cgColour1=white cgColour2=yellow cgColour3=red height=30
3 - histogram
4 - points plot
the example of all four can be seen here
the example files are
http://www.ensembl.org/info/using/external_data/examples/wiggle_plot.bed
http://www.ensembl.org/info/using/external_data/examples/wiggle_hg.bed
http://www.ensembl.org/info/using/external_data/examples/wiggle_cg.bed
http://www.ensembl.org/info/using/external_data/examples/wiggle_ta.bed
But for faster display of the big density data sets we recommend to use WIG Format (http://genome.ucsc.edu/goldenPath/help/wiggle.html)
WIG FORMAT
We support all wiggle type data formats including BED style, fixed step and variable step.
At the moment we have limited support of the wiggle track definition lines. The supported options are:
type
name
description
graphType
viewLimits
autoScale
where type is required and should be set to wiggle_0,
graphType is one of signal | colour | points | bar
for the details of configuring wiggle das track please see
http://genome.ucsc.edu/goldenPath/help/hgWiggleTrackHelp.html
example of the WIG file can be found here http://www.ensembl.org/info/using/external_data/examples/wiggle_example.wig
to view it in Ensembl
Defining Information about the Track
For each track you can define a number of properties. The following are currently supported:
- name
- A name for the track has to be unique - this is used to label the track.
- description
- A description of the track - displayed in the pop-up
- colour
- Colour of features to be rendered - may be one of: standard X11 colour map colours (e.g. red, navajowhite), a hex value (FFCC00), an RGB triple (255,204,0). Defaults to red
- url
-
Defines a URL for an external link associated with this track. This URL will be used in the details page for the track. Any '$$' in this string this will be substituted with the features identifier. There is no default for this attribute. e.g.
http://www.ensembl.org/perl/contigview?contig=$$
These are defined via a "track" line with the following format:
track attr=value
For example:
track name=BACs description="BAC ends" color=green
Location Line in the File
To ask Ensembl to go automatically to a specific chromosomal region, include these lines in the top of your file.
browser position chr:start-end
e.g.
browser position 19:6900000-7400000
How to Display Data
To display your track(s) in Ensembl's ContigView or CytoView:
- Click on the "DAS Sources" drop down menu above the main display
- Click on the "URL based data" link top pop-up a small window
- Enter the URL of your data into this box, and click "Go".
Deleting Tracks
The track will remain on your display while you navigate around the genome - to remove it, open the 'DAS' menu again. The tracks you have currently displayed will be listed. Deselect your link there. The window will close and the main Ensembl window will refresh.
Creating an Image
To create an image for a publication or your own use, click on the 'Export' roll-down menu for image export options.
Example Data Sources
-
BED: BAC end sequences: http://www.ensembl.org/info/using/external_data/examples/url_bed.txt
-
PSL: INSR Human: http://www.ensembl.org/info/using/external_data/examples/url_psl.txt
-
GFF: BAC end sequences: http://www.ensembl.org/info/using/external_data/examples/url_gff.txt
The search box at the top of the page allows you to search the help.