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Old 11-06-2019, 03:47 PM   #18
Location: Atlanta

Join Date: Nov 2018
Posts: 27

Originally Posted by samd View Post
Ok so I am guessing the "25M total reads" on Basespace actually means 50M since I did PE. Thanks for the suggestion I will look into that.

One thing I just remembered is the QC results were quite different from the first "good run" and the subsequent "bad runs". The good run has a nice skinny peak and the bad runs have lumpy peaks which I guess would be attributed to non-specific binding of primers? I've attached to the post in case anyone is interested or has any insight into that.
Again, thanks for all the feedback!
If the total reads is 25M under the indexing QC tabs in BaseSpace, it is actually the total PE reads. Under the Metrics tab, READS PF will be half of that. I would ask if they could rerun the library but at a higher concentration to target for a cluster density of around 900 K/mm2 for more reads.
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