I have two MiSeq runs of 240 samples each that act as technical replicates. To analyse, I want to denoise the runs separately, compare them, merge them, and finally remove chimeras. I’m using the dada2 plugin with qiime2 2019.4 with bash.
The only way I can think to do this involves using denoise-paired twice:
> ##Denoising
> # denoise run1
> qiime dada2 denoise-paired \
> --i-demultiplexed-seqs $Outputs/paired_end_demux_run1.qza \
> --p-trim-left-f 32 \
> --p-trunc-len-f 260 \
> --p-trim-left-r 31 \
> --p-trunc-len-r 260 \
> --p-chimera-method none \
> --p-n-threads 0 \
> --o-representative-sequences $Outputs/rep_seqs_dada2_run1.qza \
> --o-table $Outputs/table_dada2_run1.qza \
> --o-denoising-stats $Outputs/stats-dada2_run1.qza \
> --verbose
>
> #denoise run2
> qiime dada2 denoise-paired \
> --i-demultiplexed-seqs $Outputs/paired_end_demux_run2.qza \
> --p-trim-left-f 32 \
> --p-trunc-len-f 260 \
> --p-trim-left-r 31 \
> --p-trunc-len-r 260 \
> --p-chimera-method none \
> --p-n-threads 0 \
> --o-representative-sequences $Outputs/rep_seqs_dada2_run2.qza \
> --o-table $Outputs/table_dada2_run2.qza \
> --o-denoising-stats $Outputs/stats-dada2_run2.qza \
> --verbose
>
> # Summarising and comparing
> qiime feature-table summarize \
> --i-table $Outputs/table_dada2_run1.qza \
> --o-visualization $Outputs/table_dada2_run1.qzv \
> --m-sample-metadata-file $Metadata_file
> qiime feature-table summarize \
> --i-table $Outputs/table_dada2_run2.qza \
> --o-visualization $Outputs/table_dada2_run2.qzv \
> --m-sample-metadata-file $Metadata_file
>
> qiime feature-table tabulate-seqs \
> --i-data $Outputs/rep_seqs_dada2_run1.qza \
> --o-visualization $Outputs/rep_seqs_dada2_run1.qzv
> qiime feature-table tabulate-seqs \
> --i-data $Outputs/rep_seqs_dada2_run2.qza \
> --o-visualization $Outputs/rep_seqs_dada2_run2.qzv
>
> qiime metadata tabulate \
> --m-input-file $Outputs/stats-dada2_run1.qza \
> --o-visualization $Outputs/stats-dada2_run1.qzv
> qiime metadata tabulate \
> --m-input-file $Outputs/stats-dada2_run2.qza \
> --o-visualization $Outputs/stats-dada2_run2.qzv
>
> qiime quality-control evaluate-composition \
> -–i-expected-features table_dada2_run1.qza \
> -–i-observed-features table_dada2_run2.qza \
> -–p-depth 1 \
> -–o-visualization $Outputs/run_comparison.qzv
>
> ## Merging runs
> qiime feature-table merge \
> --i-tables $Outputs/table_dada2_run1.qza \
> --i-tables $Outputs/table_dada2_run2.qza \
> --o-merged-table $Outputs/table_dada2_both.qza
>
> qiime feature-table merge-seqs \
> --i-data $Outputs/rep_seqs_dada2_run1.qza \
> --i-data $Outputs/rep_seqs_dada2_run2.qza \
> --o-merged-data $Outputs/rep_seqs_dada2_both.qza
But then my merged data is only in FeatureData[Sequence] format rather than the necessary SampleData[PairedEndSequencesWithQuality] to put it back into denoise-paired. Is there another way I can do this?
Thanks!