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Old 10-13-2010, 11:54 AM   #1
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Location: Oxford

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Post 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 ?
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Old 06-03-2014, 04:03 PM   #2
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Hi Nickp,
A little bit late but 2.8 sounds wrong, the current versions are only 1.9
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Old 06-04-2014, 10:19 AM   #3
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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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barcodes, conflict, diversity, indexes, rtav2.8

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