[maker-devel] annotation stats: repeats

[Daniel Ence]

Hi Xabier, MAKER offer several options for repeat-masking. There’s a file of repetitive element proteins that is run with repeat runner, and there you can run RepeatMasker with a custom library and/or one of the default RepeatMasker libraries.

The results from these programs are in the gff3 files that maker generates. Depending on the library that you give RepeatMasker, the repeats might be classified as to transposable element family and simple vs. complex repeats. These are probably a good place to start, but you’ll have to extract that data from the gff3 file and compile it.

Let us know whether that helps.

Thanks,
Daniel





On Mar 21, 2015, at 9:27 PM, Xabier Vázquez Campos <xvazquezc at gmail.com<mailto:xvazquezc at gmail.com>> wrote:

Hi all,

I was wondering how can I get data about the repeat content of the genome from maker if possible, as well as each type of repeats: RE, transposons, simple repeats, low complexity repeats

Thank you in advance,

Xabier

--
Xabier Vázquez Campos
PhD Candidate
Water Research Centre
School of Civil and Environmental Engineering
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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