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Old 11-21-2016, 05:05 PM   #1
incognitos
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Default longest nextseq read length

Hi all,

I was wondering if anyone has any idea/experience regarding what the max read length in 1 direction for a nextseq run might be? For example, the 300 cycle kit recommends 2x150, but has anyone tried greater than 150 in 1 direction?
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Old 11-22-2016, 03:40 AM   #2
GenoMax
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One can setup asymmetric runs (know for sure with MiSeq, assume it is the same with NextSeq). So it should be possible to run 300 cycles in one direction if that is what you want. Probably would not be ideal in terms of Q-scores towards the end of the cycles.
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Old 11-22-2016, 12:45 PM   #3
Brian Bushnell
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I'm not sure whether it's possible to do >150bp runs on the NextSeq, but I am sure that I wouldn't want to go much longer.



This is a recent run on our NextSeq. Read 1 hits a 1.4% error rate on cycle 150, which is tolerable. But at that point the error rate is increasing by 50% every 30 bases, so it would be projected to hit 2.1% at 180bp, 3.15% at 210 bp, and >10% at 300bp.
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Old 12-12-2016, 02:33 PM   #4
Yepler
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Quote:
Originally Posted by GenoMax View Post
One can setup asymmetric runs (know for sure with MiSeq, assume it is the same with NextSeq). So it should be possible to run 300 cycles in one direction if that is what you want. Probably would not be ideal in terms of Q-scores towards the end of the cycles.
Yep, you can do asymmetrical runs on the NextSeq. I don't know about the length question (sorry - my run was 50/26). I *have* seen that as the sequencing proceeds, the quality goes down, so I'd be really interested to see what you get if you go for 300 cycles! Good luck.
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