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Hi all
I just had a strange result on our latest GA runs. A paired end 36 cycle run showed great Q-scores for read 1. Read 2 began with great scores, then around cycle 10, they just fell off. We had 2 runs on at the same time and it happened to both - a different lot of read 2 prep kits were used on each machine, sequencing reagents lots were the same on both and the same as for read 1. The fact that it happened to both instruments with different reagents points to maybe something we did, but I can't figure out what. Has anyone seen anything like this before or have any ideas what caused it?
I've attached a screenshot.
I just had a strange result on our latest GA runs. A paired end 36 cycle run showed great Q-scores for read 1. Read 2 began with great scores, then around cycle 10, they just fell off. We had 2 runs on at the same time and it happened to both - a different lot of read 2 prep kits were used on each machine, sequencing reagents lots were the same on both and the same as for read 1. The fact that it happened to both instruments with different reagents points to maybe something we did, but I can't figure out what. Has anyone seen anything like this before or have any ideas what caused it?
I've attached a screenshot.