<p>I ran kraken2 on a 16s rRNA sample. I get two kinds of output, one like <a href="https://drive.google.com/file/d/1uz_Ms9KBhJehIu9shzCFmbFoYy_albnY/view?usp=sharing" rel="nofollow noreferrer">this</a>
and the other one like <a href="https://drive.google.com/file/d/19vpgWaelvGsnWb7oET5y4SysKb6n4_GV/view?usp=sharing" rel="nofollow noreferrer">this</a>. So I have many files like this for each sample of my control and test group.</p>
<p>How do I generate OTU table out of these outputs for phyloseq usage? Do I parse the taxa ID column of any of these and generate a frequency table of each taxa in sample to generate OTU?</p>
<p>Any help or suggestion would be highly appreciated.</p>

CC BY-SA 4.0
2020-07-05T15:26:31.753Z
able to fix it ..issue resolved
kcm
CC BY-SA 4.0
2020-07-13T13:15:52.390Z
Can you share how you fixed this please? Having the same learning curve!
Reebola95
CC BY-SA 4.0
2022-09-02T10:48:34.210Z
Can you please add your fix / resolution as a separate answer (and accept it)? This is appearing in the question list as unanswered.
gringer
CC BY-SA 4.0
2022-09-04T08:19:35.867Z
okay may be i will close the question..
kcm
<microbial-genomics>
kraken2 output to OTU table
# kraken2 output to OTU table

(Asked by: username_0 on 2020-06-26)

I ran kraken2 on a 16s rRNA sample. I get two kinds of output, one like [this](https://drive.google.com/file/d/1uz_Ms9KBhJehIu9shzCFmbFoYy_albnY/view?usp=sharing)
and the other one like [this](https://drive.google.com/file/d/19vpgWaelvGsnWb7oET5y4SysKb6n4_GV/view?usp=sharing). So I have many files like this for each sample of my control and test group.

How do I generate OTU table out of these outputs for phyloseq usage? Do I parse the taxa ID column of any of these and generate a frequency table of each taxa in sample to generate OTU?

Any help or suggestion would be highly appreciated.

**Tags:** microbial-genomics
> **Comments:**
> **username_0**: able to fix it ..issue resolved  
> **username_1**: Can you share how you fixed this please? Having the same learning curve!  
> **username_2**: Can you please add your fix / resolution as a separate answer (and accept it)? This is appearing in the question list as unanswered.  
> **username_0**: okay may be i will close the question..  

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## 0 answers

