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I have obtained ( interspersed repeats ) libraries in the Palm plant genome. Still, unfortunately, the candidates obtained seems false positive a lot of tandem repeats found, due to denovo identifications tools I assume, then employing TRF tandem repeat finder to mask any tandem repeat, I have succeeded to mask them.

But my question here, how can I discard sequence with a belonging header, if the Candidates masked more than 40% of the full length for each of the identified candidates?

Thank you

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  • $\begingroup$ Hi @BioInfo I understand the problem, its a good question. Clearly the problem is species specific (viruses don't have tandem repeats). Could you hint as to the species please? It would be useful to know the assembler? $\endgroup$
    – M__
    Nov 26, 2020 at 10:27
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    $\begingroup$ @Michael question updated, I'm working with palm genome. $\endgroup$
    – BioInfo
    Nov 26, 2020 at 10:38
  • $\begingroup$ Thanks better, not perfect, but –Errhhh wait ... what is a "Freut plant" ... happy plant (German), "fruit plant"? I'm no wiser. $\endgroup$
    – M__
    Nov 26, 2020 at 12:15

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