Index
HiSeq 2500 System User Guide
141
SBS 26
reagents
loading 27, 29, 52, 66
loading, ICB 67
loading, SBS 81
paired end 27, 29, 66
priming 34, 58, 89
Reagents screen 24, 49, 79
recording kit ID 24, 49, 79
unloading 99
Reagents screen 24, 49, 79
Real-Time Analysis
color matrix correction 118
input files 113
log files 121
output files 113, 121
phasing 118
Q-score binning 120
quality score 119
results 121
run metrics 115
stopped run, auto resume 114
with stopped run 133
Real-Time Analysis software 7
recipe screen 75
registration, cluster locations 117
reports
first base incorporation 22, 40, 47,
64, 77, 96
review run setup screen 75
RTA.exe.config file 113
run monitoring 40, 64, 96
run setup
confirm proper flow 33, 39, 57, 63
flow cell loading 37, 61
RunInfo.xml 121-122
S
sample sheet
BaseSpace 24, 49
overview 13
SBS reagent positions 26
scan screen 75
sensor indicators 9
Sequencing Analysis Viewer 7
InterOp files 113
overview 116
sequencing consumables 18, 42, 70
sequencing modes
switching 106
show log file 10
software
about, version 10
Experiment Manager 13
HiSeq Control 12
HiSeq Control Software 7
initialization 6
Real-Time Analysis 7
Sequencing Analysis Viewer 7
show log file 10
troubleshooting 129
view full screen 10
Welcome screen 7
staggered runs 130
statistics
files 113
statistics files 113
status alert icon 10
status page 40, 64, 96
stopping a run 133
swath 22, 47, 77
switching modes 106
system check 8
T
technical assistance 143
template generation 117
tile numbering 125
troubleshooting 129
flow cell loading 129
fluidics 131
registration 117
turning off the instrument 109
U
user-supplied consumables 14
W
washes
maintenance wash 100
maintenance wash solution
preparing 100
water wash 104
water wash 8
consumables 104
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