############### 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 > =========================== =============================================================================================================================================================================================================== 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