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?
