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 ...
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. ...
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 ...
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. ...
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 ...
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 ...
"perl: warning: Setting locale failed." in RepeatMasker
I'm trying to run Repeatmasker in Linux on the command line with: ...
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 ...
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. ...
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: ...
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 ...
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 ...