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  • output is 0 for most .tbl file in repeatmasker output

    Hello

    I ran repeatmasker for my 12MB bacterial genome with rmblast and I got this result :
    ile name: kib.fa
    sequences: 1
    total length: 12113479 bp (12113479 bp excl N/X-runs)
    GC level: 67.83 %
    bases masked: 458056 bp ( 3.78 %)
    ==================================================
    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: 1973 385656 bp 3.18 %

    Total interspersed repeats: 385656 bp 3.18 %


    Small RNA: 0 0 bp 0.00 %

    Satellites: 0 0 bp 0.00 %
    Simple repeats: 1693 79440 bp 0.66 %
    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 version open-4.0.5 , sensitive mode

    run with rmblastn version 2.2.23+
    The query was compared to unclassified sequences in "kib_repeats_filtered1.fasta"
    RepBase Update 20150807, RM database version 20150

    Can anyone help me why I am getting this reulst ?

  • #2
    Moving this post to a new thread since it was not related to the original thread it was in.

    @Prianka: Keep in mind that just because a command ran (and produced output) does not mean that the output is correct/right. Based on your last posts it appeared to me that even though you had managed to run RepeatScout/Repeatmasker the analysis may not have worked right.

    Comment


    • #3
      Ok... then what would you suggest doing next ?

      Comment

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