# Export BIOM Table to TSV/CSV

**URL:** <https://forum.qiime2.org/t/export-biom-table-to-tsv-csv/585>\
**Category:** User Support\
**Tags:** biom\
**Created:** [May 10, 2017, 12:24pm UTC](https://forum.qiime2.org/t/export-biom-table-to-tsv-csv/585 "2017-05-10T12:24:48Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![akknight216](https://forum.qiime2.org/user_avatar/forum.qiime2.org/akknight216/32/102_2.png) [@akknight216](https://forum.qiime2.org/u/akknight216)\
**Post date:** [May 10, 2017, 12:24pm UTC](https://forum.qiime2.org/t/export-biom-table-to-tsv-csv/585/1 "2017-05-10T12:24:48Z")

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I'm having a similar issue. I'd like to export the feature table as a .csv, but it only gets exported as a .biom file, which doesn't seem to be compatible with phyloseq:

I've tried to import it two ways:

```bash
rich_sparse_biom = system.file("extdata", "/Users/annaknight/Documents/Microbiome/exported250/feature-table.biom", package = "phyloseq")
> rich_sparse = import_biom(rich_sparse_biom, parseFunction = parse_taxonomy_greengenes)
Error in read_biom(biom_file = BIOMfilename) : 
  Both attempts to read input file:

either as JSON (BIOM-v1) or HDF5 (BIOM-v2).
Check file path, file name, file itself, then try again.

biom_file="/Users/annaknight/Documents/Microbiome/exported250/feature-table.biom"
biomot = import_biom(biom_file)
Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
In addition: There were 50 or more warnings (use warnings() to see the first 50)

```

Do you have any suggestions on how to fix this/export as tsv/csv?

---

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**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\
**Post date:** [May 10, 2017, 12:38pm UTC](https://forum.qiime2.org/t/export-biom-table-to-tsv-csv/585/2 "2017-05-10T12:38:38Z")

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Hi @akknight216, unfortunately we can't help you with phyloseq, because that software is not developed by us. I would suggest contacting them on their [support page](https://github.com/joey711/phyloseq/issues) with any specific questions.

As far as exporting your feature table to TSV, we can modify the [instructions](https://forum.qiime2.org/t/is-there-any-way-to-summarize-taxa-plot-by-category/446/2) prepared by @jairideout:

```bash
qiime tools export table.qza --output-dir exported
biom convert -i exported/feature-table.biom -o feature-table.tsv --to-tsv

```

This uses the `biom` cli tool to [convert](http://biom-format.org/documentation/biom_conversion.html#general-usage-examples) the exported HDF5 version of the feature table to a TSV. We have discussed supporting format transformations at export time, so if/when that happens, this command most likely won't be necessary. Hope that helps!

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**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\
**Post date:** [June 10, 2017, 6:41pm UTC](https://forum.qiime2.org/t/export-biom-table-to-tsv-csv/585/3 "2017-06-10T18:41:22Z")

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