My samples run on Illumina HiSeq. I start with importing demultiplexed data using Casava 18 paired end.
So, I want to continue with DADA2, but I am not sure how to set the p-trunc-len because when I try to zoom, it becomes too large that I cannot see at what value the quality drops.
And towards the end of the plot, both forward and reverse reads showed red color. Does this means I shoud/can put p-trunc-len value at this point?
Hey there @orkid! What do you mean here:
You should be able to click and drag to form a rectangle over the area you are interested in viewing. When you release from the drag, the display will zoom in for you. Please make sure you are running the latest version of Google Chrome or Mozilla Firefox.
The summary paragraph below the plot updates depending on which base position you are hovering over, and will display an appropriate message. You can see in your screenshot above that at position 186 as longer than the smallest observed sequence, which was 158 nts.
Hope that helps!
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