This is a test version of Biostars. For the public version, visit https://www.biostars.org.
download repeats annotation file

Is there database where I can download repeats (Low-complexity regions, Tandem repeats, Complex repeats) annotation file (GFF, GTF, BED) for some organisms?

sequence annotations database

Sounds like the repeatmasker track from UCSC, does that have everything you need?

Ah, atypical species are always a problem for this sort of thing. I haven't a clue if anyone has called repeats on those. You can do it yourself, but it takes quite a bit of time.

If you have a reference genome, I would give a try to RepeatMasker. One of the outputs is a bed3-like file that you can easily subset to get an annotation file. They also have a web-server where you could try a toy example.

Thanks, as you can see it is around 2 years ago :) , in the comments I mentioned that what I need was not in server, and in this comment C: download repeats annotation file I did something similar to what you suggested.

But thank you for help.

0 answers

No answers yet.

Log in to answer this question.