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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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DNA transposons in Saccharomyces cerevisiae #173

Closed Dichopsis closed 3 years ago

Dichopsis commented 3 years ago

Hi @oushujun , I tried the EDTA pipeline on the yeast genome (Saccharomyces cerevisiae). I get TIRs and Helitrons that represent about 1% of the genome.

First, when I run RepeatMasker on the library built from EDTA, these transposable elements are all listed as DNA transposons and are not classified into subfamilies.

Secondly, in the literature it is stated that the yeast genome contains 0% DNA transposons, whereas I get 1% (number of DNA transposons: 301), but when I run RepeatModeler alone, I get 0% DNA transposons.

I was wondering how to explain these results.

Many thanks

oushujun commented 3 years ago

Hello, if you run EDTA with --anno 1 --step anno, you will get a summary file with proper superfamily info.

The low amount of TIR annotations could be false positives or previously unreported TIRs - you need to further verify them to be sure. A good start will be using TEsorter to identify conserved coding domains.

Best, Shujun

On Wed, Mar 17, 2021 at 4:04 PM Dichopsis @.***> wrote:

Hi @oushujun https://github.com/oushujun , I tried the EDTA pipeline on the yeast genome (Saccharomyces cerevisiae). I get TIRs and Helitrons that represent about 1% of the genome.

First, when I run RepeatMasker on the library built from EDTA, these transposable elements are all listed as DNA transposons and are not classified into subfamilies.

Secondly, in the literature it is stated that the yeast genome contains 0% DNA transposons, whereas I get 1% (number of DNA transposons: 301), but when I run RepeatModeler alone, I get 0% DNA transposons.

I was wondering how to explain these results.

Many thanks

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