Exporting data for further analysis in R

Last updated on 2026-10-06 | Edit this page

Overview

Questions

  • Which files are typically exported for downstream R analysis (phyloseq, DESeq2, etc.)?
  • What format conversions are required to obtain usable TSVs and tree files?

Objectives

  • Export the unrooted tree (.nwk), feature table (BIOM), taxonomy and representative sequences to a structured export folder.
  • Convert BIOM to TSV and clean headers so R packages can import tables reliably.
  • Ensure taxonomic rows and ASV columns are consistently ordered for downstream merging.

You need to export your ASV table, taxonomy table, and tree file for analyses in R. Many file formats can be accepted.

Export unrooted tree as .nwk format as required for the R package phyloseq.

BASH 

qiime tools export \
  --input-path analysis/tree/16s_unrooted_tree.qza \
  --output-path analysis/export

Create a BIOM table with taxonomy annotations. A FeatureTable[Frequency] artefact will be exported as a BIOM v2.1.0 formatted file.

BASH 

qiime tools export \
  --input-path analysis/taxonomy/16s_table_filtered.qza \
  --output-path analysis/export

Then export BIOM to TSV

BASH 

biom convert \
-i analysis/export/feature-table.biom \
-o analysis/export/feature-table.tsv \
--to-tsv

Export Taxonomy as TSV

BASH 

qiime tools export \
--input-path analysis/taxonomy/classification.qza \
--output-path analysis/export

Delete the header lines of the .tsv files

BASH 

sed '1d' analysis/export/taxonomy.tsv > analysis/export/taxonomy_noHeader.tsv
sed '1d' analysis/export/feature-table.tsv > analysis/export/feature-table_noHeader.tsv

Some packages require your data to be in a consistent order, i.e. the order of your ASVs in the taxonomy table rows to be the same order of ASVs in the columns of your ASV table. It’s recommended to clean up your taxonomy file. You can have blank spots where the level of classification was not completely resolved.

Key Points
  • Exported artefacts include: tree (Newick), feature‑table.biom, taxonomy.tsv and representative sequences if required.
  • Use biom convert to produce TSV tables and sed (or equivalent) to remove extra header lines.
  • Confirm consistent ASV order between taxonomy and table files before importing into phyloseq or other R packages.