RTA v2.8 : Conflicts with low complexity sequence

[nickp]

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 ?

[Elsie]

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

http://support.illumina.com/sequencing/sequencing_software/real-time_analysis_rta/downloads.ilmn

cheers.

[thomasblomquist]

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