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Rocketknight · 04-14-2012, 03:37 AM

That's exactly what I see, yeah. Thanks to both of you for the explanation. Should I just remove those low-quality reads and align their pairs as singletons, or should I go ahead aligning them anyway in the hopes of extracting some information from them?

Also, I noticed the per-base N content looks pretty interesting. Would I be right in saying that there was a blockage or other mishap for a few cycles (around 15-19) and that as a result the affected clusters ended up out of sync and so no longer generated a clear signal for the rest of the run?

04-14-2012, 03:37 AM	#4
Rocketknight Member Location: Ireland Join Date: Sep 2011 Posts: 86	That's exactly what I see, yeah. Thanks to both of you for the explanation. Should I just remove those low-quality reads and align their pairs as singletons, or should I go ahead aligning them anyway in the hopes of extracting some information from them? Also, I noticed the per-base N content looks pretty interesting. Would I be right in saying that there was a blockage or other mishap for a few cycles (around 15-19) and that as a result the affected clusters ended up out of sync and so no longer generated a clear signal for the rest of the run?