Questions tagged [repeatmasker]

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Build RepeatMasker default libraries beforehand (bioconda installation)

I'm using RepeatMasker on human sequences. When running RepeatMasker this way: RepeatMasker -e rmblast -species human -dir . myFile.fa RepeatMasker builds some ...
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2answers
134 views

Remove repetitive region vcf file using repeatmasker bed file [duplicate]

I have a 1000 genomes vcf file for chromosome 14. And I want to remove variants in repetitive regions flagged by repeatMasker. I have a bed file for those repeats. I downloaded that file from UCSC. ...
2
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1answer
34 views

Annotatation of transposable elements / transposons / SINE sequences in human

I need to annotate human genome with different types of information, amongst them: transposable elements. I read about repeatmasker, but what I understood is that it estimates the probability of a ...
1
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1answer
366 views

How to fix RepeatMasker.lib.nsq missing error when running RepeatModelor?

I have run RepeatModelor and I don't see the classified output file. I got this error. ...
2
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2answers
272 views

RepeatMasker annotation

I collected my own denovo library using many different tools Pipeline (structure-based ) and I updated all the headers corresponding to RepeatMasker format, to obtain Repeat coverage in the genome and ...
1
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0answers
77 views

Calculate the percentage of the genome that is represented by some sequences

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 ...
2
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1answer
213 views

"perl: warning: Setting locale failed." in RepeatMasker

I'm trying to run Repeatmasker in Linux on the command line with: ...
1
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3answers
75 views

Looking for a good tool for repeat masking in long sequences

The repeat masker site has a size limit of 90kb. Where can I mask repeats in a 500kb sequence? Ideally, I need a thorough repeat masking of known and de-novo found repeats of various complexity. I ...
2
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0answers
68 views

find repetitive elements on genome

I'm analyzing mygenome.fa with RepeatScout and RepeatMasker to find transposable elements. I produced a library of Repetitive elements with repeatscout and the I masked TE using Repeatmasker. ...
1
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0answers
101 views

repeatscout freq table

I'm running Repeatscout. I built the l-mer table called myfile.freq of myfile.fa Can anyone tell me what do they mean the second and third columns produced as output? here I report an example: ...
2
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1answer
430 views

Repeatmasker output table

I'm working with an unassembled genome of cephalopod and I would to find transposable elements. My idea is to use repeatscout to generate a library and repeatmasker to find the elements. After ...
5
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0answers
58 views

Why does repeatmasker annotate transposons of length 1?

I am working on Mac OSX. I have downloaded RepeatMasker from www.repeatmasker.org. I have downloaded RepBase from www.girinst.org. I have download the WS266 version of the C. elegans genome from ...