Questions tagged [repeat]

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2
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2answers
129 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
vote
0answers
54 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
3answers
63 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 ...
3
votes
0answers
40 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 ...
4
votes
2answers
438 views

How are centromeric/telomeric regions categorized in RepeatMasker? “Other” category?

I haven't been able to find the following in the documentation at http://www.repeatmasker.org/ (1) Why are certain regions classified as "Other"? Are these regions impossible to concretely classify ...
16
votes
1answer
495 views

How can I improve a long-read assembly with a repetitive genome?

I'm currently trying to assembly a genome from a rodent parasite, Nippostrongylus brasiliensis. This genome does have an existing reference genome, but it is highly fragmented. Here are some ...