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Run Types for TruSeq v3 Chemistry
HiSeq 2500 System User Guide
45
Run Types for TruSeq v3 Chemistry
The following table shows types of sequencing runs and the number of possible cycles for
each read when using TruSeq v3 chemistry. Use this information as a reference when
setting up the run.
Run Type Read 1
Cycles
Index 1 (i7)
Read Cycles
Index 2 (i5)
Read Cycles
Read 2
Cycles
Total
Cycles
Single-Read,
Non-Indexed
≤ 101 -- -- -- ≤ 101
Single-Read,
Single-Indexed
≤ 101 6 or 7 ¹
8 ²
-- -- ≤ 108 ¹
≤ 109 ²
Single-Read,
Dual-Indexed
≤ 101 8 8 -- ≤ 117
Paired-End,
Non-Indexed
≤ 101 -- -- ≤ 101 ≤ 202
Paired-End,
Single-Indexed
≤ 101 7 ¹
8 ²
-- ≤ 101 ≤ 209 ¹
≤ 210 ²
Paired-End,
Dual-Indexed
≤ 101 8 7 + 8 ³ ≤ 101 ≤ 225
¹ Number of cycles for single-indexed libraries
² Number of cycles for dual-indexed libraries
³ Index 2 Read of a paired-end dual-indexed run includes 7 additional chemistry-only cycles
- 2500 System 1
- User Guide 1
- Revision History 7
- Table of Contents 9
- Chapter 7 Troubleshooting 127 10
- Index 139 10
- Technical Assistance 143 10
- Overview 11
- HiSeq 2500 Components 13
- HiSeq 2500 Software 17
- Sample Sheet Overview 23
- Sequencing Consumables 25
- Perform a HiSeq v4 Run 27
- HiSeq v4 Sequencing Workflow 29
- Enter Run Parameters 31
- Load and Prime Reagents 37
- Perform a TruSeq v3 Run 51
- TruSeq v3 Sequencing Workflow 53
- Prepare Reagents for Read 2 75
- Load Reagents for Read 2 77
- Introduction 81
- Pre-Run Volume Check 85
- Perform a Rapid Run 100
- Load a Flow Cell 101
- Post-Run Procedures 107
- Unload and Weigh Reagents 109
- Perform a Maintenance Wash 111
- Perform a Water Wash 115
- Switch Sequencing Modes 117
- Shut Down the Instrument 119
- Part # 15035786 Rev. D 120
- Real-Time Analysis 121
- Real-Time Analysis Overview 123
- Monitor Run Metrics 125
- Real-Time Analysis Workflow 127
- Sequencing Output Files 131
- Output Folder Structure 133
- Tile Numbering 135
- Troubleshooting 137
- Possible Run Setup Problems 139
- Perform a Fluidics Check 141
- Stop and Resume a Run 143
- Primer Rehybridization 147
- HiSeq 2500 System User Guide 149
- Technical Assistance 153
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