text: user3332: I collected my own denovo library using many different tools Pipeline (structure-based ) and I updated all the headers corresponding to RepeatMasker format, to obtain Repeat coverage in the genome and .tbl annotation.
  when I run repeatmasker the annotation results assume to be Homosapien, where Homo annotation table ( .tbl) is limited as shown below Table (1)
  Actually my denovo repeat library consists of more than what is in the table above, example, rolling circles, Copia, Gypsy etc.. 
  RepeatMasker -Lib myOwnLibrary.fa Mygenome.fa
  
  Table (1)
  
  My question is how can I run RepeatMasker with my own library using -lib Flag and result like the table (2) below, 
  the table below assume to be vertebrates genome, this is my aim. 
  RepeatMasker -Species Vertebrates Mygenome.fa
  
  Table (2)
  
  Regards
  
  user57: After long years of just conceptual knowledge of what the software does, I was dealing with RepearMasker this week. So, I am not entirely sure I am correct, but this is how I understand it.
  The two flags you explored serve for different scenarios:
  
  -species - if the taxa/species is present in the repeat database (repBase or Dfam)
  -lib - if you want to give repeatModeler something different.
  
  In your case it seems like your library is completely missing all LINEs, SINEs and a few others. What you can do is to get from the database all repetitions of the corresponding taxa and catinate it with the repeats you are interested in (the one you supplied in the -lib argument in the first command).
  util/queryRepeatDatabase.pl -species Vertebrates > flavoured_vertebrate_repetitions.lib
  cat myOwnLibrary.fa >> flavoured_vertebrate_repetitions.lib
  RepeatMasker -lib flavoured_vertebrate_repetitions.lib Mygenome.fa
  
  This should produce annotation similar to the bottom case, but also using the repetitions you manually added.
  P.S. util/queryRepeatDatabase.pl is a script to query the database of repeats and it is shipped together with repeatModeler.
  -- edit --
  The TE classification in the summary file of repeatMasker is based on headers of the repetitive elements in the fasta file you specify in to -lib argument. So if you want to get the second-table-like, you need to somehow reclassify the repeat library to contan repBase-like classification of TEs. The explanation of lib argument from the manual:
  
  The recommended format for IDs in a custom library is:
  >repeatname#class/subclass or simply
  >repeatname#class
  In this format, the data will be processed (overlapping repeats are
    merged etc), alternative output (.ace or .gff) can be created and an
    overview .tbl file will be created. Classes that will be displayed in
    the .tbl file are 'SINE', 'LINE', 'LTR', 'DNA', 'Satellite', anything
    with 'RNA' in it, 'Simple_repeat', and 'Other' or 'Unknown' (the
    latter defaults when class is missing). Subclasses are plentiful. They
    are not all tabulated in the .tbl file or necessarily spelled
    identically as in the repeat files, so check the RepeatMasker.embl
    file for names that can be parsed into the .tbl file.
  
  
  user2893: RepeatMasker comes with a buildSummary.pl script.
  You can input the .out file from your RepeatMasker run and there is a flag to enter your species
  e.g.
  buildSummary.pl -species Vertebrates rmrun.out > mysummary.tbl
  
  In the mysummary.tbl, the summary will not assume your run to be Homo (default).
  
original_text: 3332: <p>I collected my own denovo library using many different tools Pipeline (structure-based ) and I updated all the headers corresponding to RepeatMasker format, to obtain Repeat coverage in the genome and .tbl annotation.</p>
  
  <p>when I run repeatmasker the annotation results assume to be Homosapien, where Homo annotation table ( .tbl) is limited as shown below Table (1)</p>
  
  <p>Actually my denovo repeat library consists of more than what is in the table above, example, rolling circles, Copia, Gypsy etc.. </p>
  
  <pre><code>RepeatMasker -Lib myOwnLibrary.fa Mygenome.fa
  </code></pre>
  
  <p>Table (1)</p>
  
  <p><a href="https://i.stack.imgur.com/2S9Dq.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/2S9Dq.png" alt="enter image description here"></a></p>
  
  <p>My question is how can I run RepeatMasker with my own library using -lib Flag and result like the table (2) below, </p>
  
  <p>the table below assume to be vertebrates genome, this is my aim. </p>
  
  <pre><code>RepeatMasker -Species Vertebrates Mygenome.fa
  </code></pre>
  
  <p>Table (2)</p>
  
  <p><a href="https://i.stack.imgur.com/b97Gw.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/b97Gw.png" alt="enter image description here"></a></p>
  
  <p>Regards</p>
   57: <p>After long years of just conceptual knowledge of what the software does, I was dealing with <code>RepearMasker</code> this week. So, I am not entirely sure I am correct, but this is how I understand it.</p>
  
  <p>The two flags you explored serve for different scenarios:</p>
  
  <ul>
  <li><code>-species</code> - if the taxa/species is present in the repeat database (<code>repBase</code> or <code>Dfam</code>)</li>
  <li><code>-lib</code> - if you want to give repeatModeler something different.</li>
  </ul>
  
  <p>In your case it seems like your library is completely missing all LINEs, SINEs and a few others. What you can do is to get from the database all repetitions of the corresponding taxa and catinate it with the repeats you are interested in (the one you supplied in the <code>-lib</code> argument in the first command).</p>
  
  <pre><code>util/queryRepeatDatabase.pl -species Vertebrates &gt; flavoured_vertebrate_repetitions.lib
  cat myOwnLibrary.fa &gt;&gt; flavoured_vertebrate_repetitions.lib
  RepeatMasker -lib flavoured_vertebrate_repetitions.lib Mygenome.fa
  </code></pre>
  
  <p>This should produce annotation similar to the bottom case, but also using the repetitions you manually added.</p>
  
  <p>P.S. <code>util/queryRepeatDatabase.pl</code> is a script to query the database of repeats and it is shipped together with <code>repeatModeler</code>.</p>
  
  <p>-- edit --</p>
  
  <p>The TE classification in the summary file of repeatMasker is based on headers of the repetitive elements in the fasta file you specify in to <code>-lib</code> argument. So if you want to get the second-table-like, you need to somehow reclassify the repeat library to contan repBase-like classification of TEs. The explanation of lib argument from the <a href="https://www.animalgenome.org/bioinfo/resources/manuals/RepeatMasker.html" rel="nofollow noreferrer">manual</a>:</p>
  
  <blockquote>
    <p>The recommended format for IDs in a custom library is:</p>
    
    <p>>repeatname#class/subclass or simply</p>
    
    <p>>repeatname#class</p>
    
    <p>In this format, the data will be processed (overlapping repeats are
    merged etc), alternative output (.ace or .gff) can be created and an
    overview .tbl file will be created. Classes that will be displayed in
    the .tbl file are 'SINE', 'LINE', 'LTR', 'DNA', 'Satellite', anything
    with 'RNA' in it, 'Simple_repeat', and 'Other' or 'Unknown' (the
    latter defaults when class is missing). Subclasses are plentiful. They
    are not all tabulated in the .tbl file or necessarily spelled
    identically as in the repeat files, so check the RepeatMasker.embl
    file for names that can be parsed into the .tbl file.</p>
  </blockquote>
   2893: <p>RepeatMasker comes with a buildSummary.pl script.</p>
  
  <p>You can input the .out file from your RepeatMasker run and there is a flag to enter your species</p>
  
  <p>e.g.</p>
  
  <pre><code>buildSummary.pl -species Vertebrates rmrun.out &gt; mysummary.tbl
  </code></pre>
  
  <p>In the mysummary.tbl, the summary will not assume your run to be <em>Homo</em> (default).</p>
  