[Genome] chain tracks by chromosome / strand

[Dong Xianjun]

Hi, Rachel

Thanks for your kind reply!

Before I get into the source code, I prefer to ask for some possible 
options:

--Do you have PSL files to download for the chain track?
--otherwise, do you have script to convert the database table(those in 
"Annotation database") to PSL files? (I am guessing that could be the 
way how UCSC did in order to show the chain data)

If yes for any of the above questions, I think I may save much time to 
create the track files for each chromosome (which could be a quick 
solution to split the data by chromosome.)

Thanks for help

Xianjun




Rachel Harte wrote:
> Hello Xianjun Dong,
>
> We do not have any plans to change the display of this track in this way.
> If you would like to try it out yourself, you could set up a local version
> of the Genome Browser and then you can change the display code as you
> wish. The Genome Browser source code is free for academic, non-profit and
> personal use. Here is information on dowloading the source code and
> creating a local installation:
>
> http://genome.ucsc.edu/FAQ/FAQlicense
>
> See the FAQs on "Downloading the Genome Browser source" and "Mirroring the
> Genome Browser".
>
> The chain files are in PSL format in the tables and may be downloaded from
> our downloads server: http://hgdownload.cse.ucsc.edu/downloads.html
>
> If you follow the link to the appropriate organism and then click on the
> "Annotation database" link there are downloadable files of the database
> table definitions and the data for each table e.g. chrN_chainMm8 and
> chrN_chainMm8Link files contain the data for the mouse mm8 chain tables.
> These chain tables are split up so that there is one for each chromosome.
>
> I hope that this helps you. Please let us know if you have further
> questions. We have a separate mailing list (genome-mirror at soe.ucsc.edu)
> for questions regarding mirror setup.
>
> Rachel
>
>  Rachel Harte
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
> On Thu, 19 Apr 2007, Dong Xianjun wrote:
>
>   
>> Hi,
>>
>> I am thinking whether you could offer the chain track divided by
>> chromosome and strand, for example, the chain on the same chr and same
>> trand would be put in same row, each row presents chains on different
>> chr/strand. Like,
>>
>> chr1(+): ==========     ========-----=========   =====---=====------------
>> chr2(-):              ----------=====-----------
>> -------------=========-----
>> chr3(+): ---------======== ----------
>> ======                      --------
>> chr4(+):
>> chr4(-):              ----------=====-----------     =========
>> -----=========-----
>> ......
>>
>> This would make the chain looks more readable than either of the current
>> display mode.
>>
>> Just one opinion, esp. when I felt tired of reading the genome data for
>> a whole day. Sure, it could bring more work.
>>
>> If you could offer the download link for the chains.bed file, I may be
>> able to do it by myself.
>>
>> Thanks
>>
>> --
>> ---------------------------
>> Sterding (Xianjun) Dong
>> PhD student, Boris Lenhard's group
>> Bergen Center of Computational Science
>> Bergen University, Norway
>> Mobile: 0047-47361688
>> Telephone: 0047-55276381
>> Skype: xianjun.dong
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>
>>     

-- 
---------------------------
Sterding (Xianjun) Dong
PhD student, Boris Lenhard's group
Bergen Center of Computational Science
Bergen University, Norway
Mobile: 0047-47361688
Telephone: 0047-55276381
Skype: xianjun.dong