Quality-filter for pair-end reads (16s)


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?

Thanks in advance!


16s_reads_trimmed_joined_filt_summary.qzv (305.7 KB)

Welcome to the forum @AlexL!

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).

Good luck!

Sounds great! Thank you so much for helping!

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