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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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Is EDTA suitable for Animal genomes #411

Open JINPENG-WANG opened 6 months ago

JINPENG-WANG commented 6 months ago

Hi Shujun,

I would like to use EDTA for animal genomes. What should I prepare to make EDTA suitable for Animal genomes?

Thanks very much.

Wang Jinpeng

oushujun commented 6 months ago

Depending on how you use it. Animal genomes (assuming vertebrate) have more non-LTR retrotransposons, which is not sensitively annotated by the current EDTA. You will need to provide a library for these elements to EDTA for their annotation.

Shujun

JINPENG-WANG commented 6 months ago

Thanks! I will try.

oushujun commented 5 months ago

Hello @JINPENG-WANG,

The latest EDTA (2.2.0) has better SINE/LINE support and is thus more suitable for animal genomes. Please give it a try.

Best, Shujun

JINPENG-WANG commented 1 month ago

Thanks, I will try.