Hi Steve, Yet another format to consider is bigBed: http://genome.ucsc.edu/goldenPath/help/bigBed.html
Example Three on that page shows how you can include a field-definition file (.as) to define your own custom fields. The values of those custom fields will then be displayed on the details page for each item. That will help if you want P-values, raw #'s etc to appear on the details page. You can also include the track setting "url" (described in Step 5. of http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks) if you want to link back to your own web server using the item names (4th column of BED). For large datasets, bigBed has the advantage of incremental transfer -- UCSC only fetches the parts of the file that you are viewing, as opposed to having to upload the entire file before viewing. bedDetail frees you from the limitation of having to use the item names to form the links back to your server -- you can define a completely separate ID for generating links, and include whatever text you want (including HTML) in the final column (description). It is a bit easier to generate than bigBed too, since there is no requirement to run our bedToBigBed program and make the file available on a web server or ftp server. Hope that helps, Angie ----- "Brooke Rhead" <[email protected]> wrote: > From: "Brooke Rhead" <[email protected]> > To: "Steven A Bullard" <[email protected]> > Cc: [email protected] > Sent: Tuesday, October 5, 2010 12:58:35 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] (no subject) > > Hi Steve, > > I'm not sure if you saw this reply to the list from my colleague: > > ************************* > > Hi. What you want is on genome-test, and will be coming to genome as > soon as it has been more thoroughly tested. It is a new format for > custom tracks that I call bedDetail that adds two fields to the normal > bed format to allow added information on the detail page like you > requested. > > Belinda > > ************************* > > Genome-test is our test site, and the URL for it is > http://genome-test.cse.ucsc.edu/. In general, genome-test has a lot of > untested or experimental data, so be aware of that. Instructions for > using the bedDetail format are: > > ------ > This is an extension to the BED custom tracks. BED detail format, is a > BED 4 format with 2 additional fields that are used in the detail page > display. The first additional field is an ID, which can be used in place > of the name for creating links from the detail page. The second is a > description of the item. This can be a long description including html > tables or lists to customize the display on the detail page. > > Requirements for this type of custom track are it most be uploaded from > a tab-separated file. It must have "type=bedDetail" in the track line. > > Also the name and position fields should uniquely describe an item so > that the correct id and description will be displayed on the details > page. > > Example: > Note that line breaks have been inserted into the track line in this > example for documentation display purposes. > > track name=HbVar type=bedDetail description="HbVar custom track" > url="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?display_format=page&mode=output&id=$$"; > chr11 5246919 5246920 Hb_North_York 2619 Hemoglobin variant > chr11 5255660 5255661 HBD c.1 G>A 2659 delta0 thalassemia > chr11 5247945 5247946 Hb Sheffield 2672 Hemoglobin variant > chr11 5255415 5255416 Hb A2-Lyon 2676 Hemoglobin variant > chr11 5248234 5248235 Hb Aix-les-Bains 2677 Hemoglobin variant > ------ > (from http://genome-test.cse.ucsc.edu/FAQ/FAQformat.html#format1.7) > > Please let us know if you run into any problems using the new format. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > Bullard, Steven A wrote on 10/5/10 10:53 AM: > > Hello, > > My name is Steve Bullard and I work at the University of Iowa. I am > trying to put up a custom track of our variants on chrom 9. I can get > them to upload but would like to attach data to each snp similar to what > you get when you click on those linked to dBSnp. We have our own > sequencing data and also would like to include associated P-values and > raw #'s of case control data. Is there a way to link the data to the Snp > shown. I have been working with Robert Kuhn as my PI Jeff Murray is > involved in the Facebase project and has contact with Bob. However Bob > suggested I contact his staff via this link. I have attached the file I > have been uploading to get the track basics to show up. > > > > > > > > > > Thanks, > > Steve Bullard > > > > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
