5.16 linksBed¶
Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.
5.16.1 Usage and option summary¶
Usage:
linksBed [OPTIONS] -i <BED/GFF/VCF> > <HTML file>
| Option | Description |
|---|---|
| -base | The “basename” for the UCSC browser. Default: http://genome.ucsc.edu |
| -org | The organism (e.g. mouse, human). Default: human |
| -db | The genome build. Default: hg18 |
5.16.2 Default behavior¶
By default, linksBed creates links to the public UCSC Genome Browser.
For example:
head genes.bed
chr21 9928613 10012791 uc002yip.1 0 -
chr21 9928613 10012791 uc002yiq.1 0 -
chr21 9928613 10012791 uc002yir.1 0 -
chr21 9928613 10012791 uc010gkv.1 0 -
chr21 9928613 10061300 uc002yis.1 0 -
chr21 10042683 10120796 uc002yit.1 0 -
chr21 10042683 10120808 uc002yiu.1 0 -
chr21 10079666 10120808 uc002yiv.1 0 -
chr21 10080031 10081687 uc002yiw.1 0 -
chr21 10081660 10120796 uc002yix.2 0 -
linksBed -i genes.bed > genes.html
When genes.html is opened in a web browser, one should see something like the following, where each link on the page is built from the features in genes.bed:
5.16.3 Creating HTML links to a local UCSC Browser installation¶
Optionally, linksBed will create links to a local copy of the UCSC Genome Browser.
For example:
head -3 genes.bed
chr21 9928613 10012791 uc002yip.1 0 -
chr21 9928613 10012791 uc002yiq.1 0 -
linksBed -i genes.bed -base http://mirror.uni.edu > genes.html
One can point the links to the appropriate organism and genome build as well:
head -3 genes.bed
chr21 9928613 10012791 uc002yip.1 0 -
chr21 9928613 10012791 uc002yiq.1 0 -
linksBed -i genes.bed -base http://mirror.uni.edu -org mouse -db mm9 > genes.html
