<p>You need to run <a href="https://github.com/jenniferlu717/Bracken" rel="nofollow noreferrer">Bracken</a> to the Kraken2 report output to estimate abundance.</p>

CC BY-SA 4.0
2020-11-15T14:24:55.153Z
I have multiple text file as output, and text file contains data like 2 column format with thousands of rows. from these type of outputs how do I generate OTU table
twinkle
CC BY-SA 4.0
2020-11-16T11:43:07.533Z
you will use the `--report` option output from Kraken2 like the input of Bracken for an abundance quantification of your samples. E.g. `kraken2 --db ${KRAKEN_DB} --report ${SAMPLE}.kreport ${SAMPLE}.fq > ${SAMPLE}.kraken` where **`${SAMPLE}.kreport`** will be your input for Bracken.
zorbax
CC BY-SA 4.0
2020-11-12T20:41:04.873Z
2020-11-12T20:41:04.873Z
zorbax
<p>I did run kraken2 and I get two kinds of output
How do I generate OTU table from these outputs for phyloseq usage?</p>

CC BY-SA 4.0
2020-11-12T22:34:02.540Z
Hi @twinkle if you don't get a response, maybe expand your question to provide details of your outputs? There are kraken users on the site.
M__
<genome><microbial-genomics>
kraken2 to OTU table creation
# kraken2 to OTU table creation

(Asked by: username_0 on 2020-11-12)

I did run kraken2 and I get two kinds of output
How do I generate OTU table from these outputs for phyloseq usage?

**Tags:** genome, microbial-genomics
> **Comments:**
> **username_1**: Hi @twinkle if you don't get a response, maybe expand your question to provide details of your outputs? There are kraken users on the site.  

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## 1 answers

### Answer by username_2 on 2020-11-12. Score: 1

You need to run [Bracken](https://github.com/jenniferlu717/Bracken) to the Kraken2 report output to estimate abundance.

> **Comments:**
> **username_0**: I have multiple text file as output, and text file contains data like 2 column format with thousands of rows. from these type of outputs how do I generate OTU table  
> **username_2**: you will use the `--report` option output from Kraken2 like the input of Bracken for an abundance quantification of your samples. E.g. `kraken2 --db ${KRAKEN_DB} --report ${SAMPLE}.kreport ${SAMPLE}.fq > ${SAMPLE}.kraken` where **`${SAMPLE}.kreport`** will be your input for Bracken.  

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