# Diversity analysis with OTU table text file

**URL:** https://forum.qiime2.org/t/diversity-analysis-with-otu-table-text-file/7443
**Category:** Silva
**Tags:** diversity, silva, otus, moving-pictures
**Created:** [December 13, 2018, 9:23am UTC](https://forum.qiime2.org/t/diversity-analysis-with-otu-table-text-file/7443 "2018-12-13T09:23:59Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![firefoxmicrobiom](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/f/bc8723/32.png) [@firefoxmicrobiom](https://forum.qiime2.org/u/firefoxmicrobiom)
#### Post date: [December 13, 2018, 9:23am UTC](https://forum.qiime2.org/t/diversity-analysis-with-otu-table-text-file/7443/1 "2018-12-13T09:23:59Z")

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Hello - complete newbie here. Trying to generate alpha and beta diversity core metrics from my data that I received today. I want to apply the command: qiime diversity core-metrics-phylogenetic  
however I am not sure how to generate the requisite qza files needed as inputs

What I have is a OTU table (.txt) formatted as such:  
OTU ID sample... sample.. sample... ... sample\_

a metadata file formatted as a .tsv that looks like the one from the tutorial  
and a fasta file (unaligned) (.fa)

Sequences were processes with dada2 v 1.8 and bacterial taxonomy was assigned from the Silva training set silva\_nr\_v132\_train\_set.fa.gz. Data is unfiltered.

From my understanding, this dataset is ready to proceed with steps outlined in [Overview of QIIME 2 Plugin Workflows — QIIME 2 2018.11.0 documentation](https://docs.qiime2.org/2018.11/tutorials/overview/#diversity-analysis). However, I am not able to generate the artifact files necessary to move forward (table.qza) as I do no have EMPSingleEndSequences sorted taxa.

Any idea how I would proceed? Or is it not possible with what I have been given?

Thanks for any help!

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### Author: ![jwdebelius](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jwdebelius/32/9655_2.png) [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [December 13, 2018, 9:32am UTC](https://forum.qiime2.org/t/diversity-analysis-with-otu-table-text-file/7443/2 "2018-12-13T09:32:48Z")

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Hi @firefoxmicrobiom,

Welcome!

I'd suggest converting your data to biom, using the command, `biom convert`. This is outside of QIIME, but will get the data properly formatted. So, for instance, if my table is otu\_table.txt, then I would run the comamnd,

```bash
biom convert \
 --i-input-file ./otu_table.txt \
 --o-output-pfile ./otu_table.biom \
 --to-hdf5 \
 --table-type otu_table

```

If you have taxonomy, you may want to specify that with the `--process-obs-metadata` flag.

And then checking out the [Data Import](https://docs.qiime2.org/2018.11/tutorials/importing/#feature-table-data) tutorial, specifically the section talking about feature tables.

If your unaligned fasta file is your deprelicated sequences, you're in a good place to build a tree. (Which I would highly recommend.) The data import tutorial also addresses importing the sequences.

Best of luck and happy QIIME-ING :qiime2:!

Best,  
Justine

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<div class="post-metadata">

### Author: ![firefoxmicrobiom](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/f/bc8723/32.png) [@firefoxmicrobiom](https://forum.qiime2.org/u/firefoxmicrobiom)
#### Post date: [December 13, 2018, 2:58pm UTC](https://forum.qiime2.org/t/diversity-analysis-with-otu-table-text-file/7443/3 "2018-12-13T14:58:17Z")

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I think that could work. 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: [January 13, 2019, 8:58pm UTC](https://forum.qiime2.org/t/diversity-analysis-with-otu-table-text-file/7443/4 "2019-01-13T20:58:18Z")

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