# Handoff to Qiime1 and phyloseq

**URL:** https://forum.qiime2.org/t/handoff-to-qiime1-and-phyloseq/1275
**Category:** User Support
**Tags:** export
**Created:** [September 19, 2017, 3:15am UTC](https://forum.qiime2.org/t/handoff-to-qiime1-and-phyloseq/1275 "2017-09-19T03:15:12Z")
**Posts on this page:** 6
**Page:** 1

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### Author: ![Gil\_Sharon](https://forum.qiime2.org/user_avatar/forum.qiime2.org/gil_sharon/32/8242_2.png) [@Gil\_Sharon](https://forum.qiime2.org/u/Gil_Sharon)
#### Post date: [September 19, 2017, 3:15am UTC](https://forum.qiime2.org/t/handoff-to-qiime1-and-phyloseq/1275/1 "2017-09-19T03:15:12Z")

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Hi All,

I'm trying to find the best way to combine analyses generated in Qiime2 with some functionalities from Qiime1 and Phyloseq. for than, I need the taxonomy table exported. Is there an easy way, like what's present for the biom table and phylogenetic trees, to do so (in a way that conforms with the taxonomy table format in Qiime1) ?

Thanks!  
Gil

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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: [September 19, 2017, 8:14pm UTC](https://forum.qiime2.org/t/handoff-to-qiime1-and-phyloseq/1275/3 "2017-09-19T20:14:31Z")

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Hi @Gil_Sharon! You can export your taxonomy (or any Artifact for that matter) by running `qiime tools export`:

```bash
# An example, using some test data I have hanging out on my laptop!
$ qiime tools export ~/moving-pictures/taxonomy.qza --output-dir ~/Desktop/taxa-data
$ cat ~/Desktop/taxa-data/taxonomy.tsv
Feature ID Taxon Confidence
d12759fe8dda1d65fe9077cc1ca9cf28 k __Bacteria; p__ Bacteroidetes; c __Flavobacteriia; o__ Flavobacteriales; f__[Weeksellaceae]; g__Chryseobacterium; s__ 0.9986819789023034
5ada68b9a081358e1a7d5f1d351e656a k __Bacteria; p__ Fusobacteria; c __Fusobacteriia; o__ Fusobacteriales; f __Leptotrichiaceae; g__ Leptotrichia; s__ 0.9999999985015222
d9095748835ade1b8914c5f57b6acbcf k __Bacteria; p__ Proteobacteria; c __Gammaproteobacteria; o__ Aeromonadales; f __Aeromonadaceae; g__ Oceanisphaera; s__ 0.9376999679084712
e83fa923d1e185d9c9de13ca3b37c8f2 k __Bacteria; p__ Bacteroidetes; c __Cytophagia; o__ Cytophagales; f __Cytophagaceae; g__ Flectobacillus; s__ 0.999946340028078
bc15061b61cf6b5002c58284591f97d4 k __Bacteria; p__ Firmicutes; c __Clostridia; o__ Clostridiales; f__[Mogibacteriaceae]; g__; s__ 0.9994429020230359
e063d1c3c9daf7390e5475e48d9b01c5 k __Bacteria; p__ Firmicutes; c __Clostridia; o__ Clostridiales; f __Lachnospiraceae; g__ Lachnospira; s__ 0.999998858876066
47fe572ed6a6b1d5f4a60a3884ec72e1 k __Bacteria; p__ Firmicutes; c __Bacilli; o__ Bacillales; f __Paenibacillaceae; g__ ; s__ 0.994845506178838
...

```

Depending on where you want to use this TSV table, you might need to remove the header row (e.g. QIIME 1, phyloseq)

Also, if you are interested in annotating a BIOM table with these data, you could export the `FeatureTable`, in addition to the data exported above, and use the [`biom add-metadata`](http://biom-format.org/documentation/adding_metadata.html) command to annotate the BIOM table.

Good luck, keep us posted! 🦖

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<div class="post-metadata">

### Author: ![Gil\_Sharon](https://forum.qiime2.org/user_avatar/forum.qiime2.org/gil_sharon/32/8242_2.png) [@Gil\_Sharon](https://forum.qiime2.org/u/Gil_Sharon)
#### Post date: [September 19, 2017, 9:43pm UTC](https://forum.qiime2.org/t/handoff-to-qiime1-and-phyloseq/1275/5 "2017-09-19T21:43:25Z")

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Thanks, @thermokarst!

I suppose the feature table also has the sequence for each of the amplicons?

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<div class="post-metadata">

### Author: ![Gil\_Sharon](https://forum.qiime2.org/user_avatar/forum.qiime2.org/gil_sharon/32/8242_2.png) [@Gil\_Sharon](https://forum.qiime2.org/u/Gil_Sharon)
#### Post date: [September 19, 2017, 9:43pm UTC](https://forum.qiime2.org/t/handoff-to-qiime1-and-phyloseq/1275/6 "2017-09-19T21:43:26Z")

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Never mind - got it (tutorials are a bit convoluted, but very very good, thanks! )

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<div class="post-metadata">

### Author: ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [September 19, 2017, 9:56pm UTC](https://forum.qiime2.org/t/handoff-to-qiime1-and-phyloseq/1275/7 "2017-09-19T21:56:14Z")

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Alright @Gil_Sharon! If you have thoughts on how to structure the tutorials, feel free to open a new thread, we would love to get your input! If you haven't seen this already, please check out the "[Getting Started](https://docs.qiime2.org/2017.8/getting-started/)" guide - this is our suggested "flow" for getting to know QIIME 2! Thanks!

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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: [October 21, 2017, 3:56am UTC](https://forum.qiime2.org/t/handoff-to-qiime1-and-phyloseq/1275/8 "2017-10-21T03:56:29Z")

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