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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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variation in Dad2 and QIIME2 output #777

Closed sajjadasaf closed 1 month ago

sajjadasaf commented 1 month ago

I successfully ran the pipeline and found 7,390 ASVs in the DADA2 output. However, when I checked the QIIME2 output directory, the abs-abund-table-6.tsv file showed only 884 ASVs. I'm not sure why there's such a large discrepancy between the two files. Should I proceed with the DADA2 file for downstream analysis, or should I use the QIIME2 file? Thank you for your help. I've attached the files for reference. abs-abund-table-6.csv ASV_table.csv

d4straub commented 1 month ago

Depends on your pipeline settings and aims. By default the pipeline removes everything that is taxonomic ally annotated as mitochondria or chloroplasts, see https://nf-co.re/ampliseq/2.11.0/parameters/#exclude_taxa. Maybe thats the reason? Checkout https://nf-co.re/ampliseq/2.11.0/docs/output/#pipeline-summary-report to see where ASVs were lost.

sajjadasaf commented 1 month ago

It mean that pipeline will remove everything after dada2 step. How to retain these results as we have in dada2 step. Thank you

d4straub commented 1 month ago

If you would follow the link I gave you, you would find that the solution is to use --exclude_taxa "none" .