Get documents about "Chip Library File (1LQ)
Shared by: HC121003103422
-
Stats
- views:
- 0
- posted:
- 10/3/2012
- language:
- Latin
- pages:
- 5
Document Sample
Confidential and Proprietary
AFFYMETRIX
SANTA CLARA, CA
Chip Library File (1LQ)
Specification
Author Xue Mei Zhou
Revision V2.0
Date 4/19/04
Print Name Signature Approvals Date Department
Xue Mei Zhou Chip Design Operations
Gloria Cheung Chip Design
Mike Mittmann Chip Design
Bill Kurani Quality Assurance
Chip Library File (1LQ), V2.0
Chip Library File Format Specification
Revision History
Revision Date Prepared by Change/Reason Summary
1 1/4/00 J. Retief Initial Version
2 4/19/04 XM Zhou Correction to Destype direction; first two header lines
are optional; formatting changes
9882c847-4a13-46a6-9182-0ca3b283b932.docPage 2 of 5 10/3/2012
Chip Library File (1LQ), V2.0
Chip Library File Format Specification
Table of Contents
1 INTRODUCTION ...............................................................................................................................................4
1.1 PURPOSE .........................................................................................................................................................4
1.2 AUDIENCE ......................................................................................................................................................4
1.3 SCOPE .............................................................................................................................................................4
2 1LQ FILE .............................................................................................................................................................4
2.1 1ST TWO HEADER LINES ..................................................................................................................................4
2.2 MAIN FILE ......................................................................................................................................................4
9882c847-4a13-46a6-9182-0ca3b283b932.docPage 3 of 5 10/3/2012
Chip Library File (1LQ), V2.0
Chip Library File Format Specification
1 INTRODUCTION
1.1 Purpose
This document describes the general format and the syntax for the Chip Library file (1LQ).
1.2 Audience
The intended audience of this document includes the following groups:
Chip Design Operations
Chip Design Development
Chip Design Test
Quality Assurance
1.3 Scope
The 1LQ file is generally for internal use and may be available to customers should they require more
information not contained in the CDF file.
2 1LQ File
The 1LQ file is a tab delimited text file. Blank lines are not allowed anywhere within the file. Each column
must contain a value. The same (X,Y) values may be duplicated multiple times to represent virtual
probes.
2.1 1st Two Header Lines
The first line specifies the number of rows and columns contained within the 1LQ file. The format of this
line is:
COLS/ROWS=<XGrid><TAB><YGrid><TAB>Dummy
For example:
COLS/ROWS=126 126 Dummy
The second line is a dummy line. Both header headers may be omitted.
2.2 Main File
The main file starts with a tab delimited header line, followed by the actual records.
Column Heading Type Max Description
Length
X integer X coordinate (>=0 and <= maximum XGrid)
Y integer Y coordinate (>=0 and <= maximum YGrid)
SEQUENCE string 255 Probe sequence (string of “A”, “C”, “G”, or “T”) tiled at the (X,
Y) location specified in 3’-5’ direction. “!” is used to denote
blank probe.
DESTYPE integer Design type for a given probe.
+ probe for sense target
- probe for antisense target
The following absolute values are acceptable:
0 blank probe
1 generic probe (used for Text and Center Cross)
2 primer (primers to amplicons)
3 thermodynamic control (corner checkerboards)
4 edge control
6 horizontal or vertical bar
7 normalization grid
9882c847-4a13-46a6-9182-0ca3b283b932.docPage 4 of 5 10/3/2012
Chip Library File (1LQ), V2.0
Chip Library File Format Specification
Column Heading Type Max Description
Length
10 user qc (synt check / QC)
11 automated synthesis check “extended”
12 automated synthesis check “local”
13 automated synthesis check “poly”: AAA, CCC etc.
14 cycle fidelity probe
111 perfect match (PM) expression & mapping probe
113 mismatch (MM) expression & mapping probe
102 perfect match (PM) resequencing probe
103 mismatch (MM) resequencing probe
FEATURE string 9 “control” – not used
QUALIFIER string 32 Name of the probe set; set to “default” is this is a control or
blank probe.
EXPOS long Interrogation position relative to the target.
PLEN integer Probe length. It should agree with the Length (SEQUENCE)
value.
POS integer Interrogation position relative to the Probe Sequence.
CBASE string 1 Complementary Base; same as TBase.
PBASE string 1 Base in probe at interrogation position; set to “!” for blank
probe.
TBASE string 1 Base in target at interrogation position; set to “!” for blank
probe.
IPBASE string 1 Complement of PBase.
UNIT long A unique number for each probe set. Generally, there is a 1-
1 relationship between probe set name and unit. For
resequencing designs, all sense probes have unit=1 and all
antisense probes have unit=2.
BLOCK integer -1 for unit=-1; 0 for all other unit values. This field is not
used.
ATOM integer A unique number identifying each perfect match probe and
its corresponding mismatch probe(s) within a probe set.
9882c847-4a13-46a6-9182-0ca3b283b932.docPage 5 of 5 10/3/2012
Related docs
Other docs by HC121003103422
This is a basic principle of government contracting whether monitoring performance
Views: 3 | Downloads: 0
