Affymetrix Annotation Converter 1

Affymetrix? Annotation Converter 1.0

PN 703010 Rev 1

For research use only.

Not for use in diagnostic procedures.

Trademarks Affymetrix?, GeneChip?, NetAffx?, Command Console?, Powered by AffymetrixTM, GeneChip-compatibleTM, Genotyping ConsoleTM, DMETTM, GeneTitanTM, AxiomTM, and GeneAtlasTM are trademarks or registered trademarks of Affymetrix, Inc. All other trademarks are the property of their respective owners. All other trademarks are the property of their respective owners. This database/product contains information from the Online Mendelian Inheritance in Man? (OMIM?) database, which has been obtained under a license from the Johns Hopkins University. This database/product does not represent the entire, unmodified OMIM? database, which is available in its entirety at ncbi.nlm.omim/.

Limited License Notice Limited License. Subject to the Affymetrix terms and conditions that govern your use of Affymetrix products, Affymetrix grants you a nonexclusive, non-transferable, non-sublicensable license to use this Affymetrix product only in accordance with the manual and written instructions provided by Affymetrix. You understand and agree that except as expressly set forth in the Affymetrix terms and conditions, that no right or license to any patent or other intellectual property owned or licensable by Affymetrix is conveyed or implied by this Affymetrix product. In particular, no right or license is conveyed or implied to use this Affymetrix product in combination with a product not provided, licensed or specifically recommended by Affymetrix for such use.

Patents Software products may be covered by one or more of the following patents: U.S. Patent Nos. 5,733,729; 5,795,716; 5,974,164; 6,066,454; 6,090,555; 6,185,561; 6,188,783; 6,223,127; 6,228,593; 6,229,911; 6,242,180; 6,308,170; 6,361,937; 6,420,108; 6,484,183; 6,505,125; 6510,391; 6,532,462; 6,546,340; 6,687,692; 6,607,887; 7,062,092 and other U.S. or foreign patents.

Copyright ? 2011 Affymetrix, Inc. All Rights Reserved.

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Contents

Chapter 1: Introduction........................................................................................................................................4 About This Manual .................................................................................................................................................4 Technical Support ...................................................................................................................................................4

Chapter 2: Installation and Requirements ...........................................................................................................6 Standalone Software Installation Instructions .......................................................................................................6 Minimum Hardware Requirements........................................................................................................................6 32-bit System......................................................................................................................................................6 64-bit System......................................................................................................................................................6

Chapter 3: Creating a Custom Annotation Database ...........................................................................................8 Overview .................................................................................................................................................................8 Guidelines for Creating a Text File .........................................................................................................................9 Text File Components .........................................................................................................................................9 Input File Merger Rules ................................................................................................................................... 10 Required Columns by Array Type .................................................................................................................... 13 Columns Required by Genotyping Console Functions .................................................................................... 14 Selecting and Processing Input Files.................................................................................................................... 15

Chapter 4: Accessing Annotation Converter From a Windows Command Line................................................ 20

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Chapter 1: Introduction

The Annotation Converter enables you to create custom SQLite format annotations (annot.db) for use in Affymetrix? Genotyping Console software (GTC) and Affymetrix Power Tools (APT). You can customize annotations for Affymetrix? catalog genotyping arrays or generate annotations AxiomTM custom genotyping arrays such as the Affymetrix? myDesign array plates.

The steps to create custom annotations include:

?

Download Affymetrix?-provided annot.csv file(s) from the Affymetrix website for catalog genotyping arrays

?

Download Affymetrix?-provided annot.csv file(s) and the related Annotation Converter library file package

from the myDesign webpage at the Affymetrix website

?

Create text file(s) of custom annotations (.csv, .txt, .tsv) using a text editor such as Notepad or Microsoft?

Excel?

Note: Genotyping Console 4.0 and higher, APT 1.12.0 and higher use annotation files in SQLite format (annot.db) only.

The Annotation Converter is available as a standalone application or within the Affymetrix? Genotyping Console software (GTC). It is also accessible from a Windows command line prompt.

About This Manual This manual provides step-by-step instructions that explain how to use the Annotation Converter. Screen captures may supplement the step-wise instructions to help illustrate a procedure. The screen captures in this manual may not exactly match the windows displayed on your screen.

Technical Support Affymetrix provides technical support to all licensed users via phone or e-mail.

AFFYMETRIX, INC. 3420 Central Expressway Santa Clara, CA 95051 USA Tel: (toll-free in US) 1-888-362-2447 Tel: 1-408-73105000 Fax: 1-408-731-5441 sales@ support@

AFFYMETRIX UK Ltd., Voyager, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe HP10 0HH United Kingdom

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UK and Others Tel: +44 (0) 1628-552550 France Tel: +33-08-00-91-95-05 Germany Tel: +49-01803-001334 Fax: +44 (0) 1628-552585 saleseurope@ supporteurope@

AFFYMETRIX Japan K.K. ORIX Hamamatsucho Bldg, 7F 1-24-8 Hamamatsucho, Minato-ku Tokyo 105-0013 Japan Phone: +81-(0)3-6430-4020 Fax: +81-(0)3-6430-4021 salesjapan@ supportjapan@

AFFYMETRIX China Affymetrix Shanghai Representative Office Suite 701, Shanghai Central Plaza, No. 381 Huai Hai Zhong Road Shanghai 200020, China Phone: +86-21-63915511 Fax: +86-21-63915299 supportchina@ saleschina@

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