text: user9955: I am working on a project and used the following command:
  vsearch --derep_fulllength filtered_merged.fa -sizeout -relabel Uniq -output dereplicated_filtered_merged.fa
  
  and got the following output:
  87373926 nt in 203453 seqs, min 310, max 480, avg 352
  Sorting 100%
  10981 unique sequences, avg cluster 2.0, median 1, max 1287
  Writing output file 100% 
  
  The output had provided me with the data that 10981 unique sequences have been identified. But I cant seem to identify how many reads of the most common sequence were present in the input data.
  Any suggestions will be kindly appreciated!
  
  user2108: According to the VSEARCH docs, since you have specified --sizeout your abundances have been written into the FASTA headers:
  
  --sizeout
  Take into account the abundance annotations present in the input fasta file (search for the pattern ’[>;]size=integer[;]’ in sequence headers). That option is active by default when rereplicating.
  Add abundance annotations to the output fasta file (add the pattern ’;size=integer;’ to sequence headers). If --sizein is specified, each unique sequence receives a new abun- dance value corresponding to its total abundance (sum of the abundances of its occur- rences). If --sizein is not specified, input abundances are set to 1, and each unique sequence receives a new abundance value corresponding to its number of occurrences in the input file.
  
  
original_text: 9955: <p>I am working on a project and used the following command:</p>
  <pre><code>vsearch --derep_fulllength filtered_merged.fa -sizeout -relabel Uniq -output dereplicated_filtered_merged.fa
  </code></pre>
  <p>and got the following output:</p>
  <pre><code>87373926 nt in 203453 seqs, min 310, max 480, avg 352
  Sorting 100%
  10981 unique sequences, avg cluster 2.0, median 1, max 1287
  Writing output file 100% 
  </code></pre>
  <p>The output had provided me with the data that 10981 unique sequences have been identified. But I cant seem to identify how many reads of the most common sequence were present in the input data.</p>
  <p>Any suggestions will be kindly appreciated!</p>
   2108: <p>According to the <a href="https://github.com/torognes/vsearch/releases/download/v2.15.1/vsearch_manual.pdf" rel="nofollow noreferrer">VSEARCH docs</a>, since you have specified <code>--sizeout</code> your abundances have been written into the FASTA headers:</p>
  <blockquote>
  <p>--sizeout</p>
  <p>Take into account the abundance annotations present in the input fasta file (search for the pattern ’[&gt;;]size=integer[;]’ in sequence headers). That option is active by default when rereplicating.</p>
  <p><strong>Add abundance annotations to the output fasta file (add the pattern ’;size=integer;’ to sequence headers).</strong> If --sizein is specified, each unique sequence receives a new abun- dance value corresponding to its total abundance (sum of the abundances of its occur- rences). If --sizein is not specified, input abundances are set to 1, and each unique sequence receives a new abundance value corresponding to its number of occurrences in the input file.</p>
  </blockquote>
  