text: user10386: 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
  
  
  user2388: 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.
  
  user10386: 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]       
  
  
original_text: 10386: <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>
   2388: <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>
   10386: <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>
  