[Genome] question about custom tracks

[Archana Thakkapallayil]

Hello Ge,

Thanks for the compliments on the browser. Here is the response from one 
of our developers to your questions:

1. We currently do not have any facilities for coloring items within a 
group differently.  We have had some discussions about implementing 
this, but don't have any definite plans at this point. The best option 
is to use separate items in a BED for the SNP's and the non-SNP regions 
of your blocks, then use itemRGB to color.

2. You can't override the maximum image width limitation.

3. This is a specialized track, and we don't have any general facilities 
(even internally) for this type of display.

4. You can easily setup the genome browser, within the limitations of 
our license:

"A license is required for commercial download and/or installation of 
the Genome Browser binaries and source code. No license is needed for 
academic, nonprofit, and personal use. The data displayed by the browser 
is freely available for both public and commerical use with a few 
exceptions. The README.txt file in the download directory of each 
assembly shows the use restrictions pertaining to that data set."

See this FAQ for information on licensing our source code:
        http://genome.ucsc.edu/FAQ/FAQlicense

Also, you do not need to mirror all of our data just to have the genome 
browser up and running to display your own tracks.  A reference to:
    http://genomewiki.ucsc.edu/index.php/Browser_installation
    or the source tree file: src/product/README.QuickStart
describes how to get a minimal browser up and running quickly without a 
lot of overhead.  With this, you can add your own tracks.

I hope this helps you. If you have further questions, please do not 
hesitate to contact us again.

Regards,

Archana
UCSC Genome Bioinformatics Group


Ge Zhang wrote:
> Dear Sir or Madam,
>
> First I would like to appreciate your efforts in creating and maintaining
> this excellent free resource for bioscientist. The custom track utility
> provides tremendous help to our research. I have several question about how
> to use it:
>
> 1. How to create a item with different colors? For example, if I want to
> create a item (GFF group) to show a block with several SNP markers, the
> ideal way is to use a rectangle (in light gray) for the whole block and
> several vertical lines (in black, or in different colors showing their
> functional significance) for each SNP. I try to use GFF format to describe
> such feature in the following way, but it seems to me that the Genome
> Browser will only display each feature with the color for the HIGHEST score
> (in our case, 1000 for each SNP marker).
>
> browser position chr1:213742472-213941141
> browser hide all
> track name=Block description="SNP Blocks" visibility=1 color=0,128,0
> useScore=1
> chr1    BlockFinder    Block    213753472    213759167    400    .    .
> Block_1
> chr1    BlockFinder    SNP    213743472    213743472    1000    .    .
> Block_1
> chr1    BlockFinder    SNP    213747205    213747206    1000    .    .
> Block_1
> chr1    BlockFinder    SNP    213749167    213749168    1000    .    .
> Block_1
> chr1    BlockFinder    Block    213762463    213780713    400    .    .
> Block_2
> chr1    BlockFinder    SNP    213762463    213762464    1000    .    .
> Block_2
> chr1    BlockFinder    SNP    213764076    213764077    1000    .    .
> Block_2
> chr1    BlockFinder    SNP    213769724    213769725    1000    .    .
> Block_2
> chr1    BlockFinder    SNP    213780713    213780714    1000    .    .
> Block_2
>
> 2. Is there any way to override the maximum image width limitation (5000
> pixels), because in order to display some fine features for a long genomic
> region 5000 pixels is not enough.
>
> 3. How to create a custom track showing pairwise relationship among genomic
> elements? For example the pairwise LD similar to the HapMap LD track
> included in the hg17 database (
> http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=hapmapLd).
>
> 4. In order to lower the computational loads of your site, we are thinking
> to build a stand along application using the power of Genome Browser in
> generating high quality graphic representation for genomic annotations.
> Therefore, the question is: can we use the specific codes for drawing custom
> tracks from Genome Browser and build a light-weight application instead of
> mirror the whole Genome Browser on our sever. If it is possible, what is the
> license requirement (for academic use only) and how to locate those codes?
>
> Thank you for your help!
>
> Best regards,
>
> Ge Zhang
> Center for Genome Information
> University of Cincinnati Medical Center
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>