Hi All, i understand the ITS region is very variable and so many authors do not trim but filter based on quality using trunQ and maxEE. I have seen many people use the default truncQ=2 but go as high as truncQ=10 or 15. Is there any justification for going higher. Is it better as long as you do not lose reads for example?
best wishes
Hi @Mantella86,
That's a great question! 
Due to the high variability in sequence length, filtering based on a higher truncQ score is a very reasonable thing to do. This will improve the accuracy of your maxEE cutoff to actually reflect 'real' errors in your data, instead of errors that are caused by a shorter sequence length.
If you are unsure of how high to set your truncQ score, you can always take a look at your feature table using QIIME 2 View and examine the interactive quality plot to get a better idea of where you should be filtering based on quality score.
Hope this helps!
Cheers 
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