When checking the quality score for my trimmed 16s pair-end reads, I found QC dropping to 25 at the very beginning. Though I've noticed this type of dropping previously but none has dropped below QC of 30. Should I be concerned about this? If so, any suggestions on what I shall do?
This quality drop at the 5’ end is often caused by primers or other conserved sequence at that end.
Whatever the cause, do not be concerned (it isn’t too low-quality anyway!) but you can trim it off, either using cutadapt (if you suspect or know that it is primer sequence) or with deblur (use the --p-left-trim-len parameter).