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  • RTA v2.8 : Conflicts with low complexity sequence

    We routinely use an in-line barcoding system with bases 1-4 as variable barcode nucleotides and base 5 is a mandatory T in all indexed libraries.
    We have run several such libraries under RTA 2.6 using a PhiX lane to call thresholds. An Illumina tech support suggested this might now be a problem with RTA v2.8 as it used the first 5 nucleotides to threshold rather than the first 4 that RTA2.6 used. Even with a PhiX lane for thresholding they are worried that our low complexity start to all our reads might now cause a conflict.

    Anyone else using low complexity reads in RTA 2.8 ?. Any problems over RTA 2.6 ?

  • #2
    Hi Nickp,
    A little bit late but 2.8 sounds wrong, the current versions are only 1.9

    cheers.

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    • #3
      This is indeed concerning. We synthesized our in-line barcoding reagents to have the first 4 bases be randomized followed by our less complex sequences.

      Let us all know if you have any issues going forward with the 4 base randomization and the new RTA?

      -Tom Blomquist

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