18 months ago by
VIB, Ghent, Belgium
Nothing very abnormal here.
Key thing here is that you have to think from the "other direction", the trimming of the reads usually happens on the 'end' of the read. This is due to something called read-through, meaning that your sequence reaction sequences more bases than what is in your sample and thus ends up in the primer/adapter on the other end of the read (so not the primer the seq-reaction started from, that one indeed you can't have in your read data).
Especially in the case of amplicon sequencing this happens often as the input data is rather short (or from a well defined length) , so there is a high change you end up in the primer/adapter on the other side of your read.
Combine this with the knowledge that if there are for instance only a few bases of the adapter present none of the trimming/cleaning tools will recognise these and thus they will remain in your read data given cleaned/trimmed reads of a variety of lengths.