Hi Mike,
I trained the SILVA classifier and the problem occur. But when I use the trained SILVA classifier full length. It gave a result much better. I have attached the QZV file still few sample give uncategorized bacteria 100%
If you want to make use of paired-ends from DADA2, you should run dada2 denoise paired … . DADA2 will denoise both reads and merge them for you. Alternatively you can use the deblur pipeline in place of DADA2
I tried to import the forward and reverse sequence together and used dada2 denoise paired, But no differences I noticed.
Code for import:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /scratch/amm59063/workdir/sb2_analysis/samples/fastq/both
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path /scratch/amm59063/workdir/sb2_analysis/samples/fastq/demux-paired-end.qza
code for dada2:
qiime dada2 denoise-paired
--i-demultiplexed-seqs /scratch/amm59063/workdir/sb2_analysis/samples/fastq/demux-paired-end.qza
--p-trim-left-f 8
--p-trim-left-r 7
--p-trunc-len-f 299
--p-trunc-len-r 266
--o-table /scratch/amm59063/workdir/sb2_analysis/samples/qc_paired/table.qza
--o-representative-sequences /scratch/amm59063/workdir/sb2_analysis/samples/qc_paired/rep-seqs.qza
--o-denoising-stats /scratch/amm59063/workdir/sb2_analysis/samples/qc_paired/denoising-stats.qza
Do you see anything wrong with this coding?
Thanks again
-Afaqbarplot_samples_silva.qzv (3.9 MB)
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