[Genome] affymetrix search question

[Kayla Smith]

Amrita,

We have a track in our browser for Affy U133 Plus 2 alignments.  The 
probes were aligned via the following criteria (which can also be found 
on the details page for this track):

Methods

Consensus and exemplar sequences were downloaded from the Affymetrix 
Product Support and mapped to the genome using blat followed by pslReps 
with the parameters:

    -minCover=0.3 -minAli=0.95 -nearTop=0.005

That said, you can retrive the sequence from where the probes align 
using our Table Browser ("Tables" on the blue bar of the main page) and 
the following options:

Clade: Vertebrate
genome: Human
assembly: Mar. 2006
group: Expression and Regulation
track: Affy U133 Plus2
table: affyU133Plus2
region: genome

filter:  click on "create"
   where you see "qName does match ______"  paste in your affy probe 
names.
   click submit

output format:  sequence
click "get output"

This will give you the genomic sequence for the probes you pasted in.

As far as your end result goes, we have a new Genome Graphs tool which 
you might find useful.  With this tool you could visualize (expression) 
values on a genomic scale.  Here is a FAQ to get you started: 
http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html

I hope this helps you to get the data you want.  Please don't hesitate 
to contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group




Amrita Ghosh wrote:
> Hello,
> 
> I'd like to input a list of affymetrix IDs into the BLAT server and 
> get back where those IDs fall when mapped onto a chromosome.  Would 
> this analysis be possible?
> 
> I have discovered custom track for my affy chip when going through 
> affymetrix's NetAffx website, but can I input a list of affy IDs to 
> see where they fall geometrically on the chromosome?  Ideally, I'd 
> like to set up a figure with a histogram connected to a figure of the 
> chromosome, with cytobands annotated, to show where in the chromosome 
> my expressed genes are located.
> 
> I appreciate your help.  Feel free to call and/or email me back with 
> a response or questions.
> 
> Sincerely,
>    Amrita Ghosh