Dragon ENhancers
database (DENdb)

Upload your annotation data files

add file

Using UCSC Genome Browser

To construct an annotation file and display it in the Genome Browser, follow these steps:*

Step 1. Format the data set

Formulate your data set as a tab-separated file using one of the formats supported by the Genome Browser. Annotation data can be in standard GFF format or in a format designed specifically for the Human Genome Project or UCSC Genome Browser, including bedGraph, GTF, PSL, BED, bigBed, WIG, bigWig, BAM, VCF, MAF, BED detail, Personal Genome SNP, broadPeak, narrowPeak, and microarray (BED15). GFF and GTF files must be tab-delimited rather than space-delimited to display correctly. Chromosome references must be of the form chrN (the parsing of chromosome names is case-sensitive). You may include more than one data set in your annotation file; these need not be in the same format.

Step 2. Define the Genome Browser display characteristics

Add one or more optional browser lines to the beginning of your formatted data file to configure the overall display of the Genome Browser when it initially shows your annotation data. Browser lines allow you to configure such things as the genome position that the Genome Browser will initially open to, the width of the display, and the configuration of the other annotation tracks that are shown (or hidden) in the initial display. NOTE: If the browser position is not explicitly set in the annotation file, the initial display will default to the position setting most recently used by the user, which may not be an appropriate position for viewing the annotation track.

Step 3. Define the annotation track display characteristics

Following the browser lines--and immediately preceding the formatted data--add a track line to define the display attributes for your annotation data set. Track lines enable you to define annotation track characteristics such as the name, description, colors, initial display mode, use score, etc. The track type= attribute is required for some tracks. If you have included more than one data set in your annotation file, insert a track line at the beginning of each new set of data.

 

Example 1:

Here is an example of a simple annotation file that contains a list of chromosome coordinates.

browser position chr22:20100000-20100900
track name=coords description="Chromosome coordinates list" visibility=2
chr22   20100000 20100100
chr22   20100011 20100200	
chr22   20100215 20100400
chr22   20100350 20100500
chr22   20100700 20100800
chr22   20100700 20100900

*Reference: UCSC Genome Browser