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I have construct a repeat libraries using de-novo identification methods. All results from different tools has been combined into one fasta file.

How can I get the percentage of how much these sequences are found in the original genome? That has been used earlier for repeat detections.
For example these identified candidates account for 30% from the total genome.

I used repeatmasker with a flag -lib combinLibrary.fasta mygenome.fasta but its very slow now almost one week and still far to finish.

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  • $\begingroup$ Do you want to know how much of the genome is in your sequences in a fasta file? What have you tried to do? Any perl/python/R/bash or other tools you have used or are familiar with? $\endgroup$
    – llrs
    Sep 4, 2019 at 21:36
  • $\begingroup$ i combined all the library then i used repeatmasker with a flag - lib combinLibrary.fasta mygenome.fasta . but its very slow now almost one week and still far to finish, im not sure if its right but im waiting the result while waiting i thought of asking for help $\endgroup$
    – BioInfo
    Sep 5, 2019 at 5:46
  • $\begingroup$ Great, thanks for clarifying this. I'll edit your question to include this information. You can also edit the question to add and improve the question whenever you want $\endgroup$
    – llrs
    Sep 5, 2019 at 6:59
  • $\begingroup$ i thought its easy task for the expert by using any kind of scripting language , my run still far from half time. any help please $\endgroup$
    – BioInfo
    Sep 9, 2019 at 10:00
  • $\begingroup$ Sorry I am not an expert on genome coverage. Perhaps if you link around in social networks you get more views and hopefully an answer. $\endgroup$
    – llrs
    Sep 9, 2019 at 10:19

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