[Genome] dm2 9way conservation downloads

[Ann Zweig]

Hello Casey,

	Archana passed your email along to me.  Thanks for the additional 
information; now it is quite clear what you need.

	We cannot provide a stable link for you to reference, and we cannot 
guarantee that the dm2 Conservation and Most Conserved tracks will live 
forever on the test server.  So, I would not suggest your referencing 
that server in your manuscript.

	However, I do have a solution for you.  You can create a Custom Track 
from the original dm2 Most Conserved 9-way track data and host it 
permanently on your own server.  It will display in the UCSC Genome 
Browser, but it will be fetching the data from your server.  As long as 
you leave the data on your server, the URL will be good and you can use 
it in your manuscript.

	Here are the steps for getting the data and creating a Custom Track.

1. Get the dm2 9-way Most Conserved data using the UCSC Table Browser.

   A. Navigate to the Table Browser on the genome-test server:
      http://genome-test.cse.ucsc.edu/cgi-bin/hgTables

   B. Make the following choices:
clade: Insect
genome: D. melanogaster
assembly: Apr. 2004
group: Comparative Genomics
track: Most Conserved (9)
table: phastConsElements9way
region: genome
output format: selected fields from primary and related tables
output file: name the file that will be downloaded to your computer

   C. Press "get output"
      From this page, choose every field from the table except the bin 
field.

   D. Press "get output"

The file will contain all of the data from the phastConsElements9way
table in a BED5 format.

e.g. 	

#chrom	chromStart	chromEnd	name	score
chr2L	7600	7630	lod=12	166
chr2L	7874	7898	lod=14	187
chr2L	8706	8717	lod=10	141
chr2L	8733	8768	lod=53	368
chr2L	8799	8810	lod=11	154


2. Use this data to create a Custom Track.

   A. Read this page for details about formatting a Custom Track: 
http://genome-test.cse.ucsc.edu/goldenPath/help/customTrack.html

   B. Read this page for details about creating a URL to point to your 
newly-created Custom Track: 
http://genome-test.cse.ucsc.edu/goldenPath/help/customTrack.html#SHARE


	If you have any questions about the process or the individual steps, 
please feel free to write back to the genome list.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Casey Bergman wrote:
> Hi Archana -
> 
> Thanks for this information.  I should have been more clear in saying  
> that I was interested in a stable link to data for the 9way most  
> conserved track.  There appears to be no way to download the  
> phastConsElements9way.sql & phastConsElements9way.txt.gz files, even  
> at the test site.
> 
> Is it ok to reference the following URL to the test server as a  
> stable link in a manuscript?
> <http://genome-test.cse.ucsc.edu/cgi-bin/hgTrackUi? 
> g=phastConsElements9way>
> 
> Best,
> Casey
> 
> 
> On 16 Jan 2007, at 20:39, Archana Thakkapallayil wrote:
> 
>> Hello Casey,
>>
>> The data for the 9-way alignment with dm2 are still available on  
>> our downloads server, here:
>> http://hgdownload.cse.ucsc.edu/downloads.html#fruitfly
>>
>> Also, the 9-way alignment is available on our test server at:
>> http://genome-test.cse.ucsc.edu/
>>
>> I hope this information is helpful to you. If you have further  
>> questions, please do not hesitate to contact us again.
>>
>> Regards,
>>
>> Archana
>> UCSC Genome Bioinformatics Group
>>
>> Casey Bergman wrote:
>>> Hi -
>>>
>>> I've noticed that the 15way conservation track has now replaced  
>>> the  9way track for dm2, but that the 9way track does appear  
>>> available for  download any longer.  Is this correct?  We have a  
>>> project that used  this data, and it would be good to have a  
>>> stable link to this data.   Any ideas on how this might be done?
>>>
>>> All the best,
>>> Casey Bergman, Ph.D.
>>> Faculty of Life Sciences
>>> University of Manchester
>>> Michael Smith Building
>>> Oxford Road, M13 9PT
>>> Manchester, UK
>>>
>>> Tel:  +44-(0)161-275-1713
>>> Fax: +44-(0)161-275-5082
>>> skype: caseymbergman
>>>
>>> Email: casey.bergman at manchester.ac.uk
>>> Web: http://www.bioinf.man.ac.uk/bergman/
>>>
>>>
>>> _______________________________________________
>>> 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