Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-19T15:41:49.977Z
Answers.Text: Dear, those numbers in the annotation tables not accurate, it's totally different.  i produced these tables to show an example of what I'm looking for, my repeat roughly have all type of repeats in my library file . and all the headers are suits repeatmasker analysis, ready for annotation but when u use the -lib flag the tool assume the analysis is homo and the .tbl is limited, i would like to run the annotation and obtain the second table
Answers.UserDisplayName: M.Bioinfo
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-19T15:42:19.133Z
Answers.Text: I never used repeatmodeler
Answers.UserDisplayName: M.Bioinfo
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-19T16:09:35.457Z
Answers.Text: The approach you have mentioned is beneficial if you want to combine the new de-nove library obtained with those already discovered and deposited earlier in repbase, thank you. But my question here to get more annotation details in.tbl file
Answers.UserDisplayName: M.Bioinfo
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-26T16:57:17.160Z
Answers.Text: I get it now, you asked about the labels, not about the numbers. I added info about how RM annotates them
Answers.UserDisplayName: Kamil S Jaron
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-27T10:16:41.693Z
Answers.Text: Dear thank you for the update, but I have edited all my headers earlier corresponding to the order of repeatmasker library documents, but the table still assume to be homo and limited
Answers.UserDisplayName: M.Bioinfo
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-19T15:05:52.753Z
Answers.LastActivityDate: 2020-02-26T16:54:24.577Z
Answers.LastEditDate: 2020-02-26T16:54:24.577Z
Answers.UserDisplayName: Kamil S Jaron
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-14T17:57:11.007Z
Answers.LastActivityDate: 2020-05-14T17:57:11.007Z
Answers.UserDisplayName: Tane
Body: <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.sstatic.net/2S9Dq.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/b97Gw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/b97Gw.png" alt="enter image description here"></a></p>
  
  <p>Regards</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-18T16:29:06.380Z
Comments.Text: Hello, a legit question. Could you also add the command you used to run the repeatMasker? Also, what is the second table? is it another repeatMasker run you did?
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-19T11:44:05.130Z
Comments.Text: yes. it is another run, I updated the question
Comments.UserDisplayName: M.Bioinfo
Tags: <sequence-annotation><repeat-elements><repeatmasker><repeat>
Title: RepeatMasker annotation
ThreadText: # RepeatMasker annotation
  
  (Asked by: username_0 on 2020-02-17)
  
  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)
  
  [![enter image description here](https://i.sstatic.net/2S9Dq.png)](https://i.sstatic.net/2S9Dq.png)
  
  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)
  
  [![enter image description here](https://i.sstatic.net/b97Gw.png)](https://i.sstatic.net/b97Gw.png)
  
  Regards
  
  **Tags:** sequence-annotation, repeat-elements, repeatmasker, repeat
  
  > **Comments:**
  > **username_1**: Hello, a legit question. Could you also add the command you used to run the repeatMasker? Also, what is the second table? is it another repeatMasker run you did?  
  > **username_0**: yes. it is another run, I updated the question  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2020-02-19. Score: 1 | Accepted answer
  
  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](https://www.animalgenome.org/bioinfo/resources/manuals/RepeatMasker.html):
  
  > 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.
  
  > **Comments:**
  > **username_0**: Dear, those numbers in the annotation tables not accurate, it's totally different.  i produced these tables to show an example of what I'm looking for, my repeat roughly have all type of repeats in my library file . and all the headers are suits repeatmasker analysis, ready for annotation but when u use the -lib flag the tool assume the analysis is homo and the .tbl is limited, i would like to run the annotation and obtain the second table  
  > **username_0**: I never used repeatmodeler  
  > **username_0**: The approach you have mentioned is beneficial if you want to combine the new de-nove library obtained with those already discovered and deposited earlier in repbase, thank you. But my question here to get more annotation details in.tbl file  
  > **username_1**: I get it now, you asked about the labels, not about the numbers. I added info about how RM annotates them  
  > **username_0**: Dear thank you for the update, but I have edited all my headers earlier corresponding to the order of repeatmasker library documents, but the table still assume to be homo and limited  
  
  ---
  
  ### Answer by username_2 on 2020-05-14. Score: 2
  
  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).
  
  
  ---
  
  