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.. _links:
###############
*links*
###############
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.
==========================================================================
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*
=========================== ===============================================================================================================================================================================================================
==========================================================================
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:
==========================================================================
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
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