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

Join Date: Oct 2010
Posts: 1
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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