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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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Identification of non-LTR retrotransposons #88

Closed hkchi closed 4 years ago

hkchi commented 4 years ago

Hi Shujun,

It seems that EDTA does not specifically identify LINE/SINE since EDTA_raw.pl only finds ltr|tir|helitron. Has it been benchmarked in animal genomes (e.g. human) where these elements are more prevalent?

Thanks, Kaichi

hkchi commented 4 years ago

Sorry I realized this might be duplicate of #8 and #58. I suppose that the LINE/SINE will need to be picked up by RepeatModeler/RepeatMasker in the FINAL step for animal genomes.

oushujun commented 4 years ago

We benchmarked SINE/LINE search programs in the paper using the rice genome. The performance was not satisfactory, so none of these tools were used in the EDTA pipeline. However, I didn't benchmark these tools using any animal genomes (ie. human), so I don't know whether these tools are just poor in rice or also in other genomes.