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  • Does complexity of the index read affect the quality of the insert reads?

    Hi all, does anyone know if (low) complexity in the index reads of a NovaSeq would impact the cluster alignment such that it would also affect the quality of R1/R2? Or are R1/R2 completely independent of the index reads?

  • #2
    Hello, the index complexity shouldn't affect the R1/R2. The index reads are separate from R1 and R2. Check out the results using the Sequencing Analysis Viewer after your NovaSeq runs and you can see for yourself.

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