Quality score and trimming length in DADA2
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11 months ago

I am a first-time QIIME user, and I am working with an Illumina MiSeq (2 x 300 kit) paired-end sequence. It is worth noting that both reads (R1 and R2) are presented in forward order. In addition, I used a manifest file to import the demultiplexed fastq files:- qiime tools import –type ‘SampleData[PairedEndSequencesWithQuality]’ –input-path manifest file –output-path demux_seqs.qza –source-format PairedEndFastqManifestPhred33 The sequence quality was then visualized using a qzv file (below I have attached the quality score plot of forward and reverse reads). For the denoising step, I intend to use DADA2. However, as compared to forward reads, the reverse reads have a very poor quality score. Could you perhaps suggest some trimming points for the forward and backward reading, taking the compatibility of the two reads after trimming into account? enter image description here

QIIME2 DADA2 • 323 views
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