maximilianh
commented
8 years ago This email may be useful in this context, it includes the link to the hub:
---------- Forwarded message ---------- From: Maximilian Haeussler max@soe.ucsc.edu Date: Mon, Oct 5, 2015 at 6:21 AM Subject: Re: How is file served through web pack? To: Brian Craft craft@soe.ucsc.edu, "cgl-brca@googlegroups.com" cgl-brca@googlegroups.com Cc: Molly Zhang czhang44@ucsc.edu, Maximilian Haeussler max@soe.ucsc.edu
Hi,
here is a link to a track hub I've hacked together that includes ONLY the enigma variants: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgwdev.soe.ucsc.edu/~max/brca/hub.txt
The track has just a placeholder description when you click on the features or the track name... do you have an html page I could add as a description of this track? I imagine it would be a description of BrcaExchange and Enigma, as Enigma is currently the track title.
The files for the hub are here: http://hgwdev.soe.ucsc.edu/~max/brca/ I had to write only the five little text files as described in our help docs, it's really easy: https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup
If you want to modify these files, you have to logon to hgwdev for now and modify them here /cluster/home/max/public_html/brca They're not on the brca server yet at the moment, but will eventually move there.
The links from your pages will have to look like this:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgwdev.soe.ucsc.edu/~max/brca/hub.txt&position=
Here is an example link for a single variant, with 100bp context on each side and the variant itself highlighted in pink ( you can change the color to anything else) http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgwdev.soe.ucsc.edu/~max/brca/hub.txt&position=chr17:41233443-41233644&highlight=hg19.chr17:41233543-41233544#FF69B4
cheers Max
From Max: " think it may be useful to provide the BRCA data as a genome browser track hub. It could be loaded by UCSC, Ensembl and Dalliance and allow a visual impression of the variants, relative to gene models. I've built this a while ago, the data would just have to be moved to the BRCA website and link provided somewhere on the data page."