text: user4475: I've installed Repeatscout from https://bix.ucsd.edu/repeatscout/.
  I've also installed TRF and nseg required by the program. 
  I followed the steps:
  build_lmer_table -l 16 -sequence ~/file_fasta/od_1000.fa -freq od_1000.freq
  
   RepeatScout -sequence od_1000.fa -output od_1000_repeats.fa -freq od_1000.freq -l 16
  
  and the I put this command:
  cat od_1000_repeats.fa| filter-stage-1.prl >od_1000_repeats_filt1.fa 
  
  but this message appears:
  bash: filter-stage-1.prl: command not found...
  
  Why? It is all correctly installed, I can't understand the problem
  
  user96: If you're in the RepeatScout directory you need to execute the Perl script with a ./ prefix, like so.
  cat od_1000_repeats.fa | ./filter-stage-1.prl > od_1000_repeats_filt1.fa
  
  If you're not in the RepeatScout directory, you need to provide the full relative or absolute path when executing the script. Alternatively, you can put the RepeatScout directory in your $PATH environmental variable.
  These are all standard UNIX/Linux concepts that many bioinformaticians take for granted, for better and for worse. If you're lost in all the terminology, a crash course in UNIX basics is probably where you would want to start.
  
original_text: 4475: <p>I've installed Repeatscout from <a href="https://bix.ucsd.edu/repeatscout/" rel="nofollow noreferrer">https://bix.ucsd.edu/repeatscout/</a>.
  I've also installed TRF and nseg required by the program. 
  I followed the steps:</p>
  
  <pre><code>build_lmer_table -l 16 -sequence ~/file_fasta/od_1000.fa -freq od_1000.freq
  </code></pre>
  
  <pre><code> RepeatScout -sequence od_1000.fa -output od_1000_repeats.fa -freq od_1000.freq -l 16
  </code></pre>
  
  <p>and the I put this command:</p>
  
  <pre><code>cat od_1000_repeats.fa| filter-stage-1.prl &gt;od_1000_repeats_filt1.fa 
  </code></pre>
  
  <p>but this message appears:</p>
  
  <pre><code>bash: filter-stage-1.prl: command not found...
  </code></pre>
  
  <p>Why? It is all correctly installed, I can't understand the problem</p>
   96: <p>If you're in the RepeatScout directory you need to execute the Perl script with a <code>./</code> prefix, like so.</p>
  
  <pre><code>cat od_1000_repeats.fa | ./filter-stage-1.prl &gt; od_1000_repeats_filt1.fa
  </code></pre>
  
  <p>If you're not in the RepeatScout directory, you need to provide the full relative or absolute path when executing the script. Alternatively, you can put the RepeatScout directory in your <code>$PATH</code> environmental variable.</p>
  
  <p>These are all standard UNIX/Linux concepts that many bioinformaticians take for granted, for better and for worse. If you're lost in all the terminology, a crash course in UNIX basics is probably where you would want to start.</p>
  