Probe mapping for the Human Affymetrix Exon 1.0 ST Array

[Reynolds, Regina]

To whom it may concern,

 

I am writing to enquire about probe mapping in the Affy Exon Array Track. In the description of this track, it is mentioned that the data for the track was provided by Affymetrix. I wondered if Affymetrix also provided data for probe mapping, or was mapping performed by UCSC? I know Ensembl appears to have mapped independently of the manufacturer – is this also the case for UCSC? If yes, are these annotation files publicly available for the Human GRCh37 assembly?

 

Many thanks for your help,

 

Best regards,

Regina

 

Regina H. Reynolds
UCL Class of 2020 | LWENC PhD Student

University of Copenhagen Class of 2016 | M.Sc. Molecular Biomedicine

Email: regina.re...@ucl.ac.uk | rhrey...@hotmail.co.uk  

 

[Cath Tyner]

Hello Regina,

Thank you for using the UCSC Genome Browser and for inquiring about the Affy Exon Array track on GRC37/hg19.

Data for this track were provided by Affymetrix, not by UCSC. More information about the Human Exon Array can be found here.

Annotation data from the Affy Exon Array track (and subtracks) are available from the Table Browser tool.

After going to the Table Browser, you can configure the Table Browser to obtain these data as follows:

clade: Mammal
genome: Human
assembly: GRC37/hg19
track: Affy Exon Array
table: Here you can choose any of the 10 subtracks/tables
region: genome (or you can select a region)
output format: all fields from selected table (or you can choose another drop-down option).
output file: You can enter a name of a file if you want to download the results, or leave this field blank to keep the results in the browser. 
Click "get output."

Please respond to this list if you have further questions!

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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