Color Balance
Selecting index adapters with diverse sequences for pooled libraries optimizes color balance for successful sequencing and data analysis.
When index adapter sequences are recorded in Illumina Experiment Manager (IEM), Local Run Manager, Instrument Run Setup, or BaseSpace Sequence Hub Prep tab, the software confirms that libraries in a pool have unique index combinations. However, Local Run Manager, Instrument Run Setup, and BaseSpace Sequence Hub do not check for color balance. IEM checks for color balance, but for HiSeq systems only.
Example Index Adapter Combinations
The following table provides examples of good and bad index combinations, to demonstrate color balance on a four-channel system. The good examples have signals in both channels (red and green). The bad examples are missing signal in one channel, as indicated with an X.
|
Good Examples |
Bad Examples |
||||||
|---|---|---|---|---|---|---|---|
|
Index 1 |
Index 2 |
Index 1 |
Index 2 |
||||
|
N705 |
G GA CTC CT |
S503 |
TATC C TCT |
N705 |
G GA CTC CT |
S502 |
CTCTCTAT |
|
N706 |
TAG GC AT G |
S503 |
TATC CTCT |
N706 |
TAG GC AT G |
S502 |
CTCTCTAT |
|
N701 |
TA AG GCGA |
S504 |
AGAG TAGA |
N701 |
TA AG GCGA |
S503 |
TATC CTCT |
|
N702 |
CG TA CTAG |
S504 |
AGAG TAGA |
N702 |
CG TA CTAG |
S503 |
TATC CTCT |
|
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