Answers.Body: <p>As far as I can tell, you use the <code>-lib</code> option for species where there is no existing RepeatMaster database. Therefore, all it does is attempt to locate versions of the repetitive elements from the <code>-lib</code> file in the target genome file. However, since your lib file doesn't have any information on what type of element each of your hits is, it looks like RepeatMasker is treating all of them as "Unclassified". </p>
  
  <p>Note the following from the <code>repeatmasker.help</code> file you should have downloaded along with RepeatMasker:</p>
  
  <blockquote>
    <p>The recommended format for IDs in a custom library is:</p>
    
    <p>>repeatname#class/subclass </p>
    
    <p>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).</p>
  </blockquote>
  
  <p>This makes sense. RepeatMasker cannot know if an arbitrary sequence you give it is a SINE or a LINE or anything else. It will therefore rely on the categories present in the fasta headers. Since your file has no categories, it identifies everything in your lib file as "Unknown", which is presumably what the "Unclassified" section in your output refers to:</p>
  
  <pre><code>Unclassified:    560941     66374119 bp   31.69 %
  
  Total interspersed repeats: 66374119 bp   31.69 %
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-25T12:40:46.980Z
Answers.Text: Ok, I understand the problem. In your opinion, is it possible to run with repeatmasker OB_100DEC_repeats_filtered1.fa instead of the genome.fa as fasta file and then observe the results? Could I observe any results?
Answers.UserDisplayName: jonny
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-25T13:06:07.507Z
Answers.Text: @jonny no, that would just find the same thing. I would instead try running Repeatmasker directly, setting the species to cephalopods:  `./RepeatMasker -s -species cephalopoda /home/Workdirectory/OB_100DEC.fa`
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-25T12:33:01.170Z
Answers.LastActivityDate: 2019-04-25T12:33:01.170Z
Answers.UserDisplayName: terdon
Body: <p>I'm working with an unassembled genome of cephalopod and I would to find transposable elements. My idea is to use repeatscout to generate a library and repeatmasker to find the elements. After creating a library with repeatscout,  I run Repeatmasker but it generates a table like this:</p>
  
  <pre><code> file name: OB_100DEC.fa             
  sequences:           100
  total length:  209466439 bp  (184235452 bp excl N/X-runs)
  GC level:         35.24 %
  bases masked:   73100024 bp ( 34.90 %)
  ==================================================
                 number of      length   percentage
                 elements*    occupied  of sequence
  --------------------------------------------------
  SINEs:                0            0 bp    0.00 %
        ALUs            0            0 bp    0.00 %
        MIRs            0            0 bp    0.00 %
  
  LINEs:                0            0 bp    0.00 %
        LINE1           0            0 bp    0.00 %
        LINE2           0            0 bp    0.00 %
        L3/CR1          0            0 bp    0.00 %
  
  LTR elements:         0            0 bp    0.00 %
        ERVL            0            0 bp    0.00 %
        ERVL-MaLRs      0            0 bp    0.00 %
        ERV_classI      0            0 bp    0.00 %
        ERV_classII     0            0 bp    0.00 %
  
  DNA elements:         0            0 bp    0.00 %
       hAT-Charlie      0            0 bp    0.00 %
       TcMar-Tigger     0            0 bp    0.00 %
  
  Unclassified:    560941     66374119 bp   31.69 %
  
  Total interspersed repeats: 66374119 bp   31.69 %
  
  
  Small RNA:            0            0 bp    0.00 %
  
  Satellites:           0            0 bp    0.00 %
  Simple repeats:  290711     15358198 bp    7.33 %
  Low complexity:       0            0 bp    0.00 %
  ==================================================
  
  * most repeats fragmented by insertions or deletions
    have been counted as one element
  
  
  The query species was assumed to be homo          
  RepeatMasker Combined Database: Dfam_Consensus-20181026
  
  run with rmblastn version 2.6.0+
  The query was compared to unclassified sequences in ".../OB_100DEC_repeats_filtered1.fa"
  
  </code></pre>
  
  <p>This was my command to run repeatmasker:</p>
  
  <pre><code>./RepeatMasker -s -lib /home/RepeatScout-1.0.5/OB_100DEC_repeats_filtered1.fa /home/Workdirectory/OB_100DEC.fa
  </code></pre>
  
  <p>The file <code>OB_100DEC_repeats_filtered1.fa</code> is the output of repeatscout and looks like this:</p>
  
  <pre><code>&gt;R=3 (RR=4.  TRF=0.000 NSEG=0.000)
  TAAGGCGGCGAGCTGGCAGAATCGTTAGCACGCCGGGCGAAATGCTTAGCGGTATTTCGTCTGTCTTTACGTTCTGAGTT
  CAAATTCCGCCGAGGTCGACTTTGCCTTTCATCCTTTCGGGGTCGATAAAATAAGTACCAGTTGAGCACTGGGGTCGATG
  TAATCGACTTACCCCCTCCCCCAAAATTTCTGGCCTTGTGCCTATATTAGAAACGATTATT
  &gt;R=4 (RR=5.  TRF=0.122 NSEG=0.226)
  ACACACACACACACACACACACACACATATATATATATATACATATATACGACGGGCTTCTTTCAGTTTCCGTCTACCAA
  ATCCACTCACAAGGCTTTGGTCGGCCCGAGGCTATAGTAGAAGACACTTGCCCAAGGTGCCACGCAGTGGGACTGAACCC
  GGAACCATGTGGTTGGTAAGCAAGCTACTTACCACACAGCCACTCCTGCGCCTATATATAT
  &gt;R=6 (RR=7.  TRF=0.134 NSEG=0.247)
  TTGTTTCAGTCATTTGACTGCGGCCATGCTGGAGCACCGCCTTTAGTCGAGCAAATCGACCCCAGGACTTATTCTTTGTA
  AGCCTAGTACTTATTCTATCGGTCTCTTTTGCCGAACCGCTAAGTTACGGGGACGTAAACACACCAGCATCGGTTGTCAA
  GCGATGTTGGGGGGACAAACACAGACACACAAACACACACACACACATACATATATATATATATATATATA
  &gt;R=8 (RR=9.  TRF=0.391 NSEG=0.000)`
  </code></pre>
  
  <p>and it is composed by all the TE (not classified) find in all the scaffolds of the genome.</p>
  
  <p>Can anyone explain why there are no TE?
  The fasta file that I used is only a part of the whole genome, it is about 200 mb and it is composed by the 100 greatest scaffolds of my genome.
  Maybe I made a mistake with the use of libraries. Anyway I installed RepeatMasker with rmblastn version 2.6.0+ and RepeatMasker Combined Database: Dfam_Consensus-20181026.
  thank you</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-24T22:49:16.860Z
Comments.Text: Please [edit] your question and clarify. What species are you working with? Also, you mention contigs, so should we assume the genome isn't assembled? How long are your contigs? Are they long enough to enable finding LINES? What exactly do you have in `OB_100DEC_repeats_filtered1.fa`?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-25T10:35:48.570Z
Comments.Text: I modified my post whit all the information.
Comments.UserDisplayName: jonny
Tags: <transposable-elements><repeatmasker>
Title: Repeatmasker output table
ThreadText: # Repeatmasker output table
  
  (Asked by: username_0 on 2019-04-24)
  
  I'm working with an unassembled genome of cephalopod and I would to find transposable elements. My idea is to use repeatscout to generate a library and repeatmasker to find the elements. After creating a library with repeatscout, I run Repeatmasker but it generates a table like this:
  
  ```
   file name: OB_100DEC.fa             
  sequences:           100
  total length:  209466439 bp  (184235452 bp excl N/X-runs)
  GC level:         35.24 %
  bases masked:   73100024 bp ( 34.90 %)
  ==================================================
                 number of      length   percentage
                 elements*    occupied  of sequence
  --------------------------------------------------
  SINEs:                0            0 bp    0.00 %
        ALUs            0            0 bp    0.00 %
        MIRs            0            0 bp    0.00 %
  
  LINEs:                0            0 bp    0.00 %
        LINE1           0            0 bp    0.00 %
        LINE2           0            0 bp    0.00 %
        L3/CR1          0            0 bp    0.00 %
  
  LTR elements:         0            0 bp    0.00 %
        ERVL            0            0 bp    0.00 %
        ERVL-MaLRs      0            0 bp    0.00 %
        ERV_classI      0            0 bp    0.00 %
        ERV_classII     0            0 bp    0.00 %
  
  DNA elements:         0            0 bp    0.00 %
       hAT-Charlie      0            0 bp    0.00 %
       TcMar-Tigger     0            0 bp    0.00 %
  
  Unclassified:    560941     66374119 bp   31.69 %
  
  Total interspersed repeats: 66374119 bp   31.69 %
  
  Small RNA:            0            0 bp    0.00 %
  
  Satellites:           0            0 bp    0.00 %
  Simple repeats:  290711     15358198 bp    7.33 %
  Low complexity:       0            0 bp    0.00 %
  ==================================================
  
  * most repeats fragmented by insertions or deletions
    have been counted as one element
  
  The query species was assumed to be homo          
  RepeatMasker Combined Database: Dfam_Consensus-20181026
  
  run with rmblastn version 2.6.0+
  The query was compared to unclassified sequences in ".../OB_100DEC_repeats_filtered1.fa"
  
  ```
  
  This was my command to run repeatmasker:
  
  ```
  ./RepeatMasker -s -lib /home/RepeatScout-1.0.5/OB_100DEC_repeats_filtered1.fa /home/Workdirectory/OB_100DEC.fa
  
  ```
  
  The file `OB_100DEC_repeats_filtered1.fa` is the output of repeatscout and looks like this:
  
  ```
  >R=3 (RR=4.  TRF=0.000 NSEG=0.000)
  TAAGGCGGCGAGCTGGCAGAATCGTTAGCACGCCGGGCGAAATGCTTAGCGGTATTTCGTCTGTCTTTACGTTCTGAGTT
  CAAATTCCGCCGAGGTCGACTTTGCCTTTCATCCTTTCGGGGTCGATAAAATAAGTACCAGTTGAGCACTGGGGTCGATG
  TAATCGACTTACCCCCTCCCCCAAAATTTCTGGCCTTGTGCCTATATTAGAAACGATTATT
  >R=4 (RR=5.  TRF=0.122 NSEG=0.226)
  ACACACACACACACACACACACACACATATATATATATATACATATATACGACGGGCTTCTTTCAGTTTCCGTCTACCAA
  ATCCACTCACAAGGCTTTGGTCGGCCCGAGGCTATAGTAGAAGACACTTGCCCAAGGTGCCACGCAGTGGGACTGAACCC
  GGAACCATGTGGTTGGTAAGCAAGCTACTTACCACACAGCCACTCCTGCGCCTATATATAT
  >R=6 (RR=7.  TRF=0.134 NSEG=0.247)
  TTGTTTCAGTCATTTGACTGCGGCCATGCTGGAGCACCGCCTTTAGTCGAGCAAATCGACCCCAGGACTTATTCTTTGTA
  AGCCTAGTACTTATTCTATCGGTCTCTTTTGCCGAACCGCTAAGTTACGGGGACGTAAACACACCAGCATCGGTTGTCAA
  GCGATGTTGGGGGGACAAACACAGACACACAAACACACACACACACATACATATATATATATATATATATA
  >R=8 (RR=9.  TRF=0.391 NSEG=0.000)`
  
  ```
  
  and it is composed by all the TE (not classified) find in all the scaffolds of the genome.
  
  Can anyone explain why there are no TE?
  The fasta file that I used is only a part of the whole genome, it is about 200 mb and it is composed by the 100 greatest scaffolds of my genome.
  Maybe I made a mistake with the use of libraries. Anyway I installed RepeatMasker with rmblastn version 2.6.0+ and RepeatMasker Combined Database: Dfam\_Consensus-20181026.
  thank you
  
  **Tags:** transposable-elements, repeatmasker
  
  > **Comments:**
  > **username_1**: Please [edit] your question and clarify. What species are you working with? Also, you mention contigs, so should we assume the genome isn't assembled? How long are your contigs? Are they long enough to enable finding LINES? What exactly do you have in `OB_100DEC_repeats_filtered1.fa`?  
  > **username_0**: I modified my post whit all the information.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-04-25. Score: 1 | Accepted answer
  
  As far as I can tell, you use the `-lib` option for species where there is no existing RepeatMaster database. Therefore, all it does is attempt to locate versions of the repetitive elements from the `-lib` file in the target genome file. However, since your lib file doesn't have any information on what type of element each of your hits is, it looks like RepeatMasker is treating all of them as "Unclassified".
  
  Note the following from the `repeatmasker.help` file you should have downloaded along with RepeatMasker:
  
  > 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).
  
  This makes sense. RepeatMasker cannot know if an arbitrary sequence you give it is a SINE or a LINE or anything else. It will therefore rely on the categories present in the fasta headers. Since your file has no categories, it identifies everything in your lib file as "Unknown", which is presumably what the "Unclassified" section in your output refers to:
  
  ```
  Unclassified:    560941     66374119 bp   31.69 %
  
  Total interspersed repeats: 66374119 bp   31.69 %
  
  ```
  
  > **Comments:**
  > **username_0**: Ok, I understand the problem. In your opinion, is it possible to run with repeatmasker OB_100DEC_repeats_filtered1.fa instead of the genome.fa as fasta file and then observe the results? Could I observe any results?  
  > **username_1**: @username_0 no, that would just find the same thing. I would instead try running Repeatmasker directly, setting the species to cephalopods:  `./RepeatMasker -s -species cephalopoda /home/Workdirectory/OB_100DEC.fa`  
  
  ---
  
  