Questions tagged [repeat-elements]
The repeat-elements tag has no usage guidance.
22
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Where to find the homopolymer regions bed file for Hg002 genome?
This question was also asked on Biostars
I am doing an experiment where I am trying to analyze the errors in the homopolymer regions between the polished reference hg002 genome and hifiasm assembly ...
- 19
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1
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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 ...
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Finding 2000 bp sequences that occur more than once in the genome
I am looking for a software that can identify long sequences (1500-2000 bp) that occur more than once in my genome of interest. A k-mer counter like KMC could have worked, but KMC has a max limit of ...
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Do RepeatModeler results contain functional domains?
The repeat families predicted by RepeatModeler contain known transposable elements (TEs) and unknown ones.
How do we know whether some of these may actually:
within a functional domain of a gene or
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Repeat analysis on eukaryotic assemblies
I have a hundred insect genomes and I'm looking for repeated regions along these assemblies.
First of all, I thought of using <...
- 155
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Are there any tools for discovering tandem repeats around a variant in a VCF file?
I know for example PolyX from Pierre's Jvarkit to find the number of repeated REF bases (homopolymers) around a position in a ...
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Is there a "definitive" database for Mobile Genetic Elements?
This isn't quite my speciality, but I've been tasked with finding any evidence of Mobile Genetic Elements (like transposable elements, retrotransposons, bacteriophages, etc.) within some WGS samples.
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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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Is there any way to align ChIP-seq reads to telomeres?
I know that telomeres are highly repeated sequences, but is there any way to retain any reads that map to these regions (on HG38)?
I recently managed to find some protein binding to centromeres, ...
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150
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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 ...
- 386
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161
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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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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 ...
- 2,469
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Finding transposable elements using RepeatMasker
I'm using RepeatMasker to detect, classify the Transposable elements. My Input is a eukaryotic non-reference genome.
I made a run via RepeatMasker many times to Mask the TEs, but return 0 Annotation ...
- 386
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103
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Detect gene duplication events from a whole genome in FASTA format
Are there any tools for finding duplications from a whole genome in FASTA format?
Let's say the genome has gene A duplicated somewhere in the genome and gene B triplicated in tandem elsewhere in the ...
- 2,469
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TRAL does not find "Phobos result file"
I want to use TRAL to annotate tandem repeats in the reference genome of Caenorhabditis elegans. For this, I need to install some external software, such as Phobos. I've downloaded Phobos and I am ...
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