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Part # 15050091 Rev. C
Color Matrix Correction
After registration and intensity extraction, RTA v2 corrects for cross talk between channels.
Cross talk occurs when a cluster shows intensity in the C channel and some intensity also
shows in the A channel, for example. Using a 4 x 4 color matrix, RTA v2 generates matrix-
corrected intensities with reduced or no cross talk, and balances differences in overall
intensity between color channels.
Empirical Phasing Correction
During the sequencing reaction, each DNA strand in a cluster extends by 1 base per cycle.
Phasing and prephasing occurs when a strand becomes out of phase with the current
incorporation cycle.
}
Phasing occurs when a base falls behind.
}
Prephasing occurs when a base jumps ahead.
Figure 25
Phasing and Prephasing
A
Read with a base that is phasing
B
Read with a base that is prephasing
RTA v2 corrects the effects of phasing and prephasing using the empirical phasing
correction algorithm, which maximizes the cumulative correction values at every cycle
throughout the run.
Phasing and prephasing results are recorded in the file named EmpiricalPhasing_[lane]_
[read]_[tile].txt, which is located in the folder
Data\Intensities\BaseCalls\Phasing
.