Answers.Body: <p>I actually went back to the output folder on the MiniSeq and found this file: <code>DemultiplexSummaryF1L1</code>, which contains demultiplexing information of the whole run. Half-way through this file I found what I was looking for:</p>
  <pre><code>### Most Popular Index Sequences                        
  
  ### Columns: Sequence ReverseComplement HitCount                        
  
  Index                       
  TGACCA  TGGTCA  2455964             
  CGATGT  ACATCG  2320579             
  GGCCCC  GGGGCC  2023652             
  CGCGGG  CCCGCG  1983605             
  CCGTCC  GGACGG  1641274         
  CAGATC  GATCTG  1514252             
  CCGGCC  GGCCGG  1319383             
  CCGCGC  GCGCGG  1109940             
  ACAGTG  CACTGT  891344      
  CCCGGG  CCCGGG  706083              
  TGCCCA  TGGGCA  168294              
  CAGCTC  GAGCTG  164091  
  .... [data continues]       
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-18T14:02:17.940Z
Answers.LastActivityDate: 2021-05-18T14:02:17.940Z
Answers.UserDisplayName: justinian482
Answers.Body: <p>I don't know that you can get them from that file.  I've noticed that when the Miseq is left to run its version of fastq generation software, there are no indices in the undetermined file.  I usually run bcl2fastq myself if I want that information.</p>
  <p>They recently came out with a new version of software for the MiSeq, so things might be different now.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-17T17:11:07.090Z
Answers.LastActivityDate: 2021-05-17T17:11:07.090Z
Answers.UserDisplayName: swbarnes2
Body: <p>I recently did some sequencing on a MiniSeq and unexpectedly the <code>Undetermined_S0_L001_R1_001.fastq.gz</code> file contained quite a lot of data (about 40% of total). I would like to know which indices are present in this file and ideally get a frequency of all index sequences in this file. How can I do this?</p>
  <p>This is the output of <code>head</code>:</p>
  <pre><code>@MN00148:128:000H2YCW2:1:11102:12116:1065 1:N:0:0
  GNAGAGGATTCAGGGAGCCAGCGCGCATATATCAG
  +
  F#FFFFFFFFFFFFFFFFFFA=/A///////////
  @MN00148:128:000H2YCW2:1:11102:11354:1065 1:N:0:0
  GNACCCGTGCGGCTGGAGAGACCACTAGAAAGAAT
  +
  A#AFFFFFFFFFFFFFFFFF///////FF=////6
  @MN00148:128:000H2YCW2:1:11102:4103:1066 1:N:0:0
  ANGTTGGTGGTACATCAGGGACGCGGAGATCTCAG
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-17T17:07:02.337Z
Comments.Text: How did you demultiplex? With bcl2fastq? You can generate the index reads like `I1`
Comments.UserDisplayName: Chris_Rands
Tags: <ngs><sequence-analysis><fastq><demultiplexing><indexing>
Title: Get frequency of index sequences of fastq file
ThreadText: # Get frequency of index sequences of fastq file
  
  (Asked by: username_0 on 2021-05-17)
  
  I recently did some sequencing on a MiniSeq and unexpectedly the `Undetermined_S0_L001_R1_001.fastq.gz` file contained quite a lot of data (about 40% of total). I would like to know which indices are present in this file and ideally get a frequency of all index sequences in this file. How can I do this?
  
  This is the output of `head`:
  
  ```
  @MN00148:128:000H2YCW2:1:11102:12116:1065 1:N:0:0
  GNAGAGGATTCAGGGAGCCAGCGCGCATATATCAG
  +
  F#FFFFFFFFFFFFFFFFFFA=/A///////////
  @MN00148:128:000H2YCW2:1:11102:11354:1065 1:N:0:0
  GNACCCGTGCGGCTGGAGAGACCACTAGAAAGAAT
  +
  A#AFFFFFFFFFFFFFFFFF///////FF=////6
  @MN00148:128:000H2YCW2:1:11102:4103:1066 1:N:0:0
  ANGTTGGTGGTACATCAGGGACGCGGAGATCTCAG
  
  ```
  
  **Tags:** ngs, sequence-analysis, fastq, demultiplexing, indexing
  
  > **Comments:**
  > **username_1**: How did you demultiplex? With bcl2fastq? You can generate the index reads like `I1`  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2021-05-18. Score: 1 | Accepted answer
  
  I actually went back to the output folder on the MiniSeq and found this file: `DemultiplexSummaryF1L1`, which contains demultiplexing information of the whole run. Half-way through this file I found what I was looking for:
  
  ```
  ### Most Popular Index Sequences                        
  
  ### Columns: Sequence ReverseComplement HitCount                        
  
  Index                       
  TGACCA  TGGTCA  2455964             
  CGATGT  ACATCG  2320579             
  GGCCCC  GGGGCC  2023652             
  CGCGGG  CCCGCG  1983605             
  CCGTCC  GGACGG  1641274         
  CAGATC  GATCTG  1514252             
  CCGGCC  GGCCGG  1319383             
  CCGCGC  GCGCGG  1109940             
  ACAGTG  CACTGT  891344      
  CCCGGG  CCCGGG  706083              
  TGCCCA  TGGGCA  168294              
  CAGCTC  GAGCTG  164091  
  .... [data continues]       
  
  ```
  
  
  ---
  
  ### Answer by username_2 on 2021-05-17. Score: 1
  
  I don't know that you can get them from that file. I've noticed that when the Miseq is left to run its version of fastq generation software, there are no indices in the undetermined file. I usually run bcl2fastq myself if I want that information.
  
  They recently came out with a new version of software for the MiSeq, so things might be different now.
  
  
  ---
  
  