Questions tagged [repeatmasker]
The repeatmasker tag has no usage guidance.
12
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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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2
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506
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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. ...
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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 ...
- 43
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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.
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465
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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 ...
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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 ...
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3
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319
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"perl: warning: Setting locale failed." in RepeatMasker
I'm trying to run Repeatmasker in Linux on the command line with:
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4
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127
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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 ...
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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.
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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:
...
- 171
2
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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 ...
- 171
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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 ...
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