[Genome] changing default display size on genome browser

[Brooke Rhead]

Hello again Charleston,

A colleague came up with another solution.  If you have a list of SNP 
identifiers of interest, you could make a custom track of those SNPs 
with some padding on either side, then select the custom track in the 
Table Browser with the output format "hyperlinks to Genome Browser" 
option selected.  This will give you a clickable list of your SNPs that 
will open a new Genome Browser centered around the SNP you clicked.

To do this, first go to the Table Browser and select the SNP track and 
table.  Paste the list of rsIDs in the "identifiers (names/accessions):" 
field.  Choose "selected fields" output and get the fields chrom, 
chromStart, chromEnd, and name.  At this point you will need to use your 
own program (or send your results to the Galaxy website) to subtract 
some number (1,000 say) from chromStart and add to chromEnd.

Now you can take that data and re-upload it as a custom track.  You can 
hit the "add custom track" button on the main Genome Browser page and 
paste the data there to create the custom track.

To get a list of hyperlinks, go back to the Table Browser, select the 
custom track you just made, and choose "hyperlinks to Genome Browser" as 
the output format.  Now you should have a list of links that will go to 
each SNP, with 2,000 bases surrounding it (if you added and subtracted 
1,000 bases from either end in the previous step).

Note that with this method, the SNP of interest will no longer be 
highlighted in the Genome Browser unless you previously entered it into 
the position/search box.  However, it will be centered in the Genome 
Browser display.

I hope this information helps.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Brooke Rhead wrote:
> Hello Charleston,
> 
> The padding of 250 bases on either side of a SNP is a setting that we 
> configure here, and it is applicable to all users.  There is not a way 
> to change that setting on your end (unless you want to set up a mirror 
> of the Genome Browser).
> 
> There are a couple of work-arounds you might try.  First, another way to 
> zoom out quickly with a single click is to click on the bands in the 
> chromosome ideogram above the Genome Browser display.  This will zoom 
> out the display to the width of the band you click in the chromosome 
> image.  However, this might be too drastic -- the image will likely be 
> zoomed out too far.  Another possibility, if you are working with a 
> particular gene and have one of the gene tracks turned on, is to click 
> on a gene that encompasses your SNP, and then on the gene details page, 
> click on the "position" link.  This will zoom you out to the level of 
> the gene.  (Note that for the "UCSC Genes" track, the position link is 
> under the "Sequence and Links to Tools and Databases" section and is 
> simply called "Genome Browser".)
> 
> I hope this information is useful.  If you have further questions, 
> please do not hesitate to contact us again.
> 
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
> 
> 
> 
> Chiang, Charleston Wen-Kai wrote:
>> Hi,
>>
>> When I searched the genome browser for a SNP (say, rs363153) in the
>> search box at the Gateway page, the first screen I get to is the
>> display of a region 501 bps long (250 bps left and right of the SNP).
>> Is there a way to change the default setting such that this initial
>> screen would display a larger area around the SNP, so that I will not
>> have to zoom out multiple times every time I searched a SNP.
>>
>> Some specification:
>  > browser: firefox 2.0.0.7
>  > os: windows XP
>> Sincerely, Charleston 
>  >
>  > _______________________________________________
>>  Genome maillist  -  Genome at soe.ucsc.edu 
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> _______________________________________________
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