<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>

CC BY-SA 4.0
2019-09-04T21:36:47.747Z
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?
llrs
CC BY-SA 4.0
2019-09-05T05:46:19.633Z
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
M.Bioinfo
CC BY-SA 4.0
2019-09-05T06:59:57.613Z
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
llrs
CC BY-SA 4.0
2019-09-09T10:00:13.260Z
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
M.Bioinfo
CC BY-SA 4.0
2019-09-09T10:19:38.307Z
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.
llrs
CC BY-SA 4.0
2019-09-11T02:23:47.933Z
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.
Edward Kirton
CC BY-SA 4.0
2020-02-12T11:21:15.013Z
@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.
M.Bioinfo
<database><repeat-elements><repeatmasker><repeat>
Calculate the percentage of the genome that is represented by some sequences
# 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**: @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.  

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## 0 answers

