illumina HiSeq X, User Manual, Page: 81 / 86

In
d
e
x
HiSeq X System User Guide
71
Index
%
%PF 57
A
activity indicators 10
available disk space 14, 48
B
base call files 53, 60
base calling
cycle 3 57
quality score 57
BaseSpace 2
data transfer 54
run monitoring 21
sample sheet 23
sample sheets 15
storage and analysis 21
bcl2fastq software 53
binning Q-scores 21
C
chastity filter 57
chemistry steps, monitoring 37
cluster intensities 37, 56
cluster location
files 53, 60
template generation 55
clusters passing filter 57
color matrix correction 56
components
flow cell compartment 3, 5
fluidics compartment 3
optics module 3
reagent compartment 3-4
config file, Real-Time Analysis 53
config file, RTA v2 61
confirm first base 22
confirm proper flow, default values 31,
36
consumables
Illumina sequencing kits 18
preparation 18
user supplied 7
cross talk 56
customer support 75
cycles, monitoring 37
D
data compression 59
data transfer
network specifications 54
disk space, checking 14
documentation 16, 75
DoNotEject drive 8
dual-surface imaging 2
dual indexing
on paired-end flow cell 23
settings on recipe screen 23
E
empirical phasing 56
error probability 58
errors and warnings
in output files 54
status icons 11
experiment name 22
F
filter files 53, 60
first base incorporation
confirmation 37
report 22
first base report 37
flow cell
flow cell holder 27