Body: <p>I have construct a repeat libraries using de-novo identification methods. All  results from different tools has been combined into one fasta file.</p>
  
  <p>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.<br>
  For example these identified candidates account for 30% from the total genome. </p>
  
  <p>I used repeatmasker with a flag <code>-lib combinLibrary.fasta mygenome.fasta</code> but its very slow now almost one week and still far to finish. </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-04T21:36:47.747Z
Comments.Text: 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?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-05T05:46:19.633Z
Comments.Text: 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
Comments.UserDisplayName: M.Bioinfo
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-05T06:59:57.613Z
Comments.Text: 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
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-09T10:00:13.260Z
Comments.Text: 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
Comments.UserDisplayName: M.Bioinfo
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-09T10:19:38.307Z
Comments.Text: 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.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-11T02:23:47.933Z
Comments.Text: how many repeats do you have?  have you tried repeatmasker with a smaller set to validate your method?  This would allow you to estimate time to completion for the full dataset.  Have you dereplicated your repeats?  That may be necessary/useful depending on how collected them, since you didn't give any details.
Comments.UserDisplayName: Edward Kirton
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-12T11:21:15.013Z
Comments.Text: @EdwardKirton I collected the repeats using a structure-based method, each class of TEs detected with a different tool, after validation and discarding false positive, all the results merged in one fasta file, now my question is to know the coverage of this repeat occured in the whole genome.
Comments.UserDisplayName: M.Bioinfo
Tags: <database><repeat-elements><repeatmasker><repeat>
Title: Calculate the percentage of the genome that is represented by some sequences
ThreadText: # Calculate the percentage of the genome that is represented by some sequences
  
  (Asked by: username_0 on 2019-09-04)
  
  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.
  
  **Tags:** database, repeat-elements, repeatmasker, repeat
  
  > **Comments:**
  > **username_1**: 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?  
  > **username_0**: 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  
  > **username_1**: 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  
  > **username_0**: 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  
  > **username_1**: 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.  
  > **username_2**: how many repeats do you have?  have you tried repeatmasker with a smaller set to validate your method?  This would allow you to estimate time to completion for the full dataset.  Have you dereplicated your repeats?  That may be necessary/useful depending on how collected them, since you didn't give any details.  
  > **username_0**: @username_2 I collected the repeats using a structure-based method, each class of TEs detected with a different tool, after validation and discarding false positive, all the results merged in one fasta file, now my question is to know the coverage of this repeat occured in the whole genome.  
  
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  ## 0 answers
  
  