Hello! I'm analysing metabarcoding sequence data of fungi using ITS. I received these sequences from someone else and some things have been a bit of a mystery...
I have been looking for the primers in my reads and have found that while the forward primer is always found in the expected orientation in the forward and reverse reads, the reverse primer is sometimes found in the unexpected orientation both in the forward, and the reverse reads.
These are the results of searching for the primers in 2 samples:
I considered that perhaps there may be contamination in there somewhere, perhaps there was some reverse primer in with the forward reads? But this would not explain the reverse orientation of the reverse primer found in the reverse reads...
