Linking To A Specific Genome In Jbrowse

Question

[Biowoogles]

I am looking for some options as to how I might be able to dynamically control and link to an installation of JBrowse I have running on a server from another webpage, for example:

I have a page on a site that gives information about a particular contig of a genome, and I would like to be able to link to the JBrowse visualisation of the contig sequence with some annotation data as a track. Is there a way to do this using using the url api or another similarly easy method, or if not, could you advise me on the nature of the script I would have to write (I am capable of writing something in JS or Python) to get this to work?

[girlwithglasses]

Have you asked your question on the JBrowse mailing list? See http://gmod.org/wiki/JBrowse#Contacts_and_Mailing_Lists

Answer 1

[cmdcolin]

There are a lot of ways to link to specific genome regions using the URL which is documented here

http://gmod.org/wiki/JBrowse_Configuration_Guide#Controlling_JBrowse_with_the_URL_Query_String

You can use

• http://localhost/jbrowse/?loc=chr1
• http://localhost/jbrowse/?loc=chr1:100..200
• http://localhost/jbrowse/?loc=GENEID

Those are all options. Linking to the specific chr region is available automatically, and linking to a specific GENEID works if you have run generate-names.pl on your dataset.