I used cutadapt to search a set of single-ended demultiplexed sequences for my specified adapters using the forward primer sequence (--p-front), the reverse complement of the reverse primer sequence (--p-adapter), while adding a few other parameters to allow for IUPAC nucleotide reading (--p-match-r…

Hi @emmzee , The trim cuts sequences from the 5' direction while truncate trims from the 3'. The values you set refer to the position in the sequences. Given your barplots you would really only need to worry about the truncating value. The 5' values look good enough. Although, the DADA2 tutorials d…

dada2

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How to denoise samples so less is lost with chimera removal?