Thanks for this tutorial. I have one question: does ITSxpress assume that primers/barcodes have been removed from sequences? e.g. do I need to use cutadapt before trimming with ITSexpress?
I normally use demultiplexed reads. You certainly don’t need to remove primers from the 5’ ends because they get chopped off when ITSxpress finds the ITS region. Removing read through primers, or other junk from the 3’ end could potentially improve merging depending on the insert size, read length and read quality. Since Dada2 uses overlap to calibrate its model you don’t want to trim to much off the 3’ just for being lower quality, you can always do that later with Dada2 settings.
Thanks! I will try and use my reads as they are, and if I have issues with merging I will consider removing read through primers.