Hi.
first I have 13 paired-end meat samples. and the kind of sequencing is 16S Ribosomal RNA Gene Amplicons for the Illumina MiSeq System. I imported them by creating a manifest file and get this file.
then I trimmed the adapters and primers by this command:
qiime cutadapt trim-paired \
-- i- *demultiplexed-sequences paired-end-demux.qza *
--p-front-f CCTACGGGNGGCWGCAG **
--p-front-r GACTACHVGGGTATCTAATCC **
*--p-match-adapter-wildcards *
*--p-match-read-wildcards *
*--p-discard-untrimmed *
--o-trimmed-sequences paired-end-demux-trimmed.qza
based on this discussion cutadapt . this is about the primers if you can check the command.
after cutadapt these are the results: paired-end-demux-trimmed.qzv (315.7 KB)
then I was confused to decide on dada2 parameters but finally I decided to use just forward reads (please correct me I'm doing wrong) with this command:
*qiime dada2 denoise-single *
*--i-demultiplexed-seqs paired-end-demux-trimmed.qza *
--p-trim-left 10 **
--p-trunc-len 280 **
*--o-representative-sequences rep-seqs-dada2.qza *
*--o-table table-dada2.qza *
--o-denoising-stats stats-dada2.qza
but after that the mean of passed reads was about 50% while in other studies I know they do this with about 70%-80% passed.
sorry for long message and thank you for your help in advance.