I recently imported paired end reads into Qiime2 and saw an unusual pattern with the reverse reads. As you can see in the below image the first 40 bp of the reverse reads have a broad error range. Does anyone know what may be causing this?
Hi @mradz,
Welcome to the 
forum!
The dark region is the 25-75th quartile on your data (all the lines are boxplots) and the dashed are the range. So, it looks like you have a high degree variability in those first 40 bp. If it were my data, I would definitely trim those to limit issues. I might also think about trimming the end of my reverse read, too, since you have a clear drop off in quality there.
Best,
Justine
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