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Old 05-17-2013, 11:53 AM   #7
Senior Member
Location: USA

Join Date: Jul 2012
Posts: 184

I don't think the adapters were the problem. As the others have said, you were way too overclustered in that lane. You can try upping the mismatch rate or playing with the failed reads to get some more data back, but the chances of getting even 50% of your data back are pretty slim.

Next time you encounter overclustering in your flow cell, I would suggest immediately performing a strip and rehyb of your primers and restarting the run. This will usually lower the cluster density a little bit.
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