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  • ReapeatMasker only LINE SINE Simple_region

    Hi all,
    does anyone know how I can only mask mammal LINE, SINE and simple repeats??
    I think the "-noint" option is not masking full LINEs and SINEs. Am I right? I tried with
    Code:
    RepeatMasker -par 20 -no_is -species mammal#LINE -species mammal#SINE -species mammal#SimpleRepeat file..fasta
    and
    Code:
    RepeatMasker -par 20 -no_is -species mammal -class LINE -class SINE -class SimpleRepeat file.fasta
    Can anyone help me?

  • #2
    Okay, if anyone is interested,... I think there is no option like that implemented. I parsed the mammalian DB and created a new lib only with LINEs and SINEs. Then instead of -species mammal used -lib own_lib.

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