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Old 12-07-2017, 07:34 AM   #4
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Location: Atlanta

Join Date: Dec 2017
Posts: 4

Originally Posted by finswimmer View Post

Read 2 und 3 are the index read. As they have just a few cycles the Q30 is alway higher than in Read 1 und 4.

What was the Cluster density? Have you had better runs before? What kind of gDNA do you try to sequence (human?) ? Maybe you have low diversity in your target regions, which makes it hard for the MiSeq to distiginguish the clusters . Spike in phiX might help.

fin swimmer

The cluster density was very high 1600 K/mm2 (supposed to be 1000-1200 K/mm2 for V2 reagents).
Yes, I have had better runs but the cluster density has always been in the upper limit. I am sequencing bacterial gDNA from several species.
Maybe this is low diversity. How can I double check that in the run parameters?

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