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Old 04-15-2018, 10:49 AM   #2
josh kinman
Location: Austin

Join Date: Apr 2014
Posts: 61

It looks like your Q scores have a big drop at ~80bp which indicates that you have a lot of smaller than expected library fragments. Since you are sequencing v3-v4 libraries I would guess this is due to amplified primer dimer, most likely in the libraries that got the higher read representation which you should see when looking at the data.

This wouldn't hurt the pass filter rate since that is calculated at read 25.
Did you visualize these libraries before sequencing?
Josh Kinman
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