Hi @jwdebelius,
Excuse me again, I continue having some problems.
Finally I chose only to work with forward sequences due to low quality scores in the reverse.
My barplot looks as follows, with a lot of unassigned sequences in some samples.
Here, my scripts:
qiime cutadapt demux-single
--i-seqs MULTIPLEXED_SINGLE/multiplexed-seqs.qza
--m-barcodes-file MULTIPLEXED_SINGLE/metadata.tsv
--m-barcodes-column Barcode
--p-error-rate 0
--o-per-sample-sequences MULTIPLEXED_SINGLE/demultiplexed-seqs.qza
--o-untrimmed-sequences MULTIPLEXED_SINGLE/untrimmed.qza
--verbose
It seems strange to me the low percentage that indicates with adapters?
qiime cutadapt trim-single
--i-demultiplexed-sequences MULTIPLEXED_SINGLE/demultiplexed-seqs.qza
--p-front GTGCCAGCMGCCGCGGTAA
--p-front GGACTACHVGGGTWTCTAAT
--p-error-rate 0
--o-trimmed-sequences MULTIPLEXED_SINGLE/trimmed-seqs3.qza
--verbose
qiime dada2 denoise-single
--i-demultiplexed-seqs Gut_microbiota/MicrobiotaPerro/MULTIPLEXED_SINGLE/trimmed-seqs3.qza
--p-trim-left 20
--p-trunc-len 220
--p-n-threads 2
--o-table MULTIPLEXED_SINGLE/table3FORW.qza
--o-representative-sequences MULTIPLEXED_SINGLE/rep-seqs3FORW.qza
--o-denoising-stats MULTIPLEXED_SINGLE/denoising-stats3FORW.qza
--verbose
denoising-stats3FORW.qza :
qiime feature-classifier classify-consensus-vsearch
--i-query MULTIPLEXED_SINGLE/rep-seqs3FORW.qza
--i-reference-reads ref-seqs97.qza
--i-reference-taxonomy ref-taxonomy- silva_132_97_16S.qza
--o-classification MULTIPLEXED_SINGLE/taxonomy-vsearch.qza
In taxonomy-vsearch I don't see many unassigned:
I appreciate your review and guidance, I don't know how to continue.
Thank you so much