Questions tagged [repeat-elements]

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19
votes
6answers
2k views

Are there any RepBase alternatives for genome-wide repeat element annotations?

I’m using the RepBase libraries in conjunction with RepeatMasker to get genome-wide repeat element annotations, in particular for transposable elements. This works well enough, and seems to be the de ...
14
votes
2answers
341 views

Finding the location and unit length of repetitive sequences within a long read

After discovering a few difficulties with genome assembly, I've taken an interest in finding and categorising repetitive DNA sequences, such as this one from Nippostrongylus brasiliensis [each base is ...
8
votes
1answer
362 views

Counting repeated kmers sequences that match at least x % of reads sequence

Working on a fastQ file, I would like to get the occurrences of repeated sequences for all possible kmers of a given length that cover at least 90% of the read's length for the whole data set. ...
8
votes
1answer
901 views

How can I use Nanopore reads to close gaps or resolve repeats in a short-read assembly?

Low coverage MinION reads should be useful to close gaps and resolve repeats left by short-read assemblers. However, I haven't had any success with the software I know about. I'm aware of the ...
6
votes
2answers
557 views

Is it wise to use RepeatMasker on prokaryotes?

I'm looking for a way to identify low complexity regions and other repeats in the genome of Escherichia coli. I found that RepeatMasker may be used for example when drafting genomes of prokaryotes (E. ...
5
votes
0answers
57 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 ...
3
votes
2answers
512 views

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 ...
3
votes
1answer
35 views

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 ...
3
votes
1answer
66 views

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 ...
3
votes
1answer
613 views

Aligning ChIP-Seq reads to repeats for downstream peak analysis

This is a brief question regarding the above. I have previously used bowtie to map reads from paired-end ChIP-Seq sequencing, then used the positions for peak-calling. However, I'm trying to do ...
2
votes
1answer
183 views

What does "motif 2 bp or longer" mean?

I'm reading a preprint on a new somatic variant discovery tool, and the first sentence of the Discussion section has me confused. Across the four datasets analyzed in this study, we discovered that ...
2
votes
1answer
32 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 ...
2
votes
2answers
51 views

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. ...
2
votes
2answers
254 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 ...
2
votes
2answers
99 views

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, ...
2
votes
0answers
22 views

Do RepeatModeler results contain functional domains?

The repeat families predicted by RepeatModeler contain known TEs and unknown ones. How do we know whether some of these may actually be a functional domain of a gene? It's predicted as repeats may ...
1
vote
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 ...
1
vote
2answers
50 views

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 ...
1
vote
0answers
15 views

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 <...
1
vote
0answers
76 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 ...
1
vote
0answers
91 views

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 ...