[Genome] question about URL construction

[jing_gao at agilent.com]

Hi,

Thanks for the help on this topic in the past. I'm still having a little problem here with constructing the URL and have the bed file loaded up to your browser properly.

I'm attaching my test bed file here. When I loads it directly into your browser by going to your web site and do it manually, everything is beautiful. This is the UCSC URL I'm seeing from the browser:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=93311163&Submit=go+to+genome+browser&position=chrX%3A000000007-000000054


When I load it in using a constructed URL, there are 2 problems. This is my constructed URL:
http://genome.ucsc.edu/cgi-bin/hgTracks??org=human&position=chrX&hgt.customText=https://wcosned2.cos.agilent.com/earray/userdata/probedesign/PI1234/output/GenomeTiling_bed


Problems:

1. How do I add the position like: position=chrX%3A000000007-000000054

This gives the preferred resolution, but what is "3A"? How do I get that string for all chromosomes and all organisms?


2. Bigger problem, if you click on my URL you may see, on top of the page, there is an error line:

Unrecognized format line 1 of custom track: https://wcosned2.cos.agilent.com/earray/userdata/probedesign/PI1234/output/GenomeTiling_bed (note: chrom names are case sensitive)


Why? The same file loads OK within your browser, why not with my URL?


A million thanks.


Jing



 <<GenomeTiling_bed>> 

Jing Gao MD PhD
Sr. R&D Engineer/Scientist
Agilent Technologies
5301 Stevens Creek Rd
Santa Clara, CA 95051
Tel: (408) 553-2571
Email: jing_gao at agilent.com




-----Original Message-----
From: Donna Karolchik [mailto:donnak at soe.ucsc.edu] 
Sent: Thursday, May 03, 2007 1:47 PM
To: Galt Barber
Cc: jing_gao at agilent.com; Genome
Subject: Re: [Genome] question about URL construction

You have to be a bit careful when you use the db parameter -- it 
depends on what you want from your URL. If you want the URL to 
always point to that specific assembly version, it's better to use 
the db name. However, if you want your URL to always point to the 
latest assembly version for a genome (i.e. automatically use the 
newer version if an assembly is updated), then you should use the 
org name.

-Donna

----- Original Message ----- 
From: "Galt Barber" <galt at soe.ucsc.edu>
To: "Donna Karolchik" <donnak at soe.ucsc.edu>
Cc: <genome at soe.ucsc.edu>; <jing_gao at agilent.com>
Sent: Thursday, May 03, 2007 1:40 PM
Subject: Re: [Genome] question about URL construction


>
> You can usually just specify the db (e.g. hg18) in the URL
> (URL=http://server/path/...&db=hg18...), and the system
> will figure out the org automatically.
>
> -Galt
>
>
> On Thu, 3 May 2007, Donna Karolchik wrote:
>
>> hi Jing,
>>
>> To add to what Galt says, if you are using one of the org names
>> that contains white space (e.g. D. melanogaster), be sure to 
>> put a
>> "+" in place of the white space, i.e. D.+melanogaster.
>>
>> -Donna
>> -----------------------------------
>> Donna Karolchik
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>> ----- Original Message -----
>> From: "Galt Barber" <galt at soe.ucsc.edu>
>> To: <jing_gao at agilent.com>
>> Cc: <genome at soe.ucsc.edu>
>> Sent: Thursday, May 03, 2007 1:31 PM
>> Subject: Re: [Genome] question about URL construction
>>
>>
>> >
>> > Check out name, description, organism, etc. in dbDB in this
>> > file:
>> >
>> > http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql
>> >
>> > -Galt
>> >
>> >
>> > On Thu, 3 May 2007 jing_gao at agilent.com wrote:
>> >
>> >> Hi,
>> >>
>> >>
>> >>
>> >> I'm trying to figure out how to construct an URL to share my
>> >> annotation tracks with others. I'm following your 
>> >> instruction
>> >> on
>> >> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#SHARE,
>> >>
>> >> Which works well for human. And I could figure out org=mouse
>> >> and org=rat.
>> >>
>> >>
>> >>
>> >> But could you tell me the String values I should use for 
>> >> "org="
>> >> in the case for the following species:
>> >>
>> >>
>> >>
>> >> A. thaliana
>> >>
>> >> C. elegans
>> >>
>> >> D. melanogaster
>> >>
>> >> D. rerio
>> >>
>> >> G. gallus
>> >>
>> >> H. sapiens        human
>> >>
>> >> M. musculus     mouse
>> >>
>> >> R. norvegicus   rat
>> >>
>> >> S. cerevisiae
>> >>
>> >> S. pombe
>> >>
>> >> X. tropicalis
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Thank you very much.
>> >>
>> >>
>> >>
>> >> Jing
>> >>
>> >> _______________________________________________
>> >> Genome maillist  -  Genome at soe.ucsc.edu
>> >> http://www.soe.ucsc.edu/mailman/listinfo/genome
>> >>
>> > _______________________________________________
>> > Genome maillist  -  Genome at soe.ucsc.edu
>> > http://www.soe.ucsc.edu/mailman/listinfo/genome
>> >
>>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>