text: user4475: 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
  
  user298: 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 %
  
  
original_text: 4475: <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>
   298: <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>
  