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7.5 years ago
Medhat
9.7k
Is there database where I can download repeats (Low-complexity regions, Tandem repeats, Complex repeats) annotation file (GFF, GTF, BED) for some organisms?
Sounds like the repeatmasker track from UCSC, does that have everything you need?
I used https://genome-euro.ucsc.edu/cgi-bin/hgTables and it can give simple repeats only, also rice and trypanosoma do not exist; any Idea or suggestion?
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.
I think this what I will do followed by A: Convert repeat masked out file to bed file format then I will have my BED file
Repeat database from Rice genome. Perhaps this for trypanosoma?
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.