Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-15T14:24:55.153Z
Answers.Text: 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
Answers.UserDisplayName: twinkle
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-16T11:43:07.533Z
Answers.Text: 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.
Answers.UserDisplayName: zorbax
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-12T20:41:04.873Z
Answers.LastActivityDate: 2020-11-12T20:41:04.873Z
Answers.UserDisplayName: zorbax
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-12T22:34:02.540Z
Comments.Text: 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.
Comments.UserDisplayName: M__
Tags: <genome><microbial-genomics>
Title: kraken2 to OTU table creation
ThreadText: # 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 @username_0 if you don't get a response, maybe expand your question to provide details of your outputs? There are kraken users on the site.  
  
  ---
  
  ## 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.  
  
  ---
  
  