search

oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
315 stars 70 forks source link

Can this tool be used in the genomes of bacteria, archaea and fungi? #405

Closed RuolinHe closed 7 months ago

RuolinHe commented 7 months ago

Hi Ou,

I knew this tool is designed for high eukaryotic genomes such as plants and animals.

And I am curious whether I can use this tool in the genomes of bacteria, archaea and fungi.

Looking forward to your reply.

Best wishes, Ruolin He

oushujun commented 7 months ago

Someone tried in fungi and need to use the —force 1 parameter. I am not sure in archaea and maybe not in bacteria. You probably need to use copy-number based approaches to achieve higher confidence for these smaller genomes

Shujun

On Mon, Nov 27, 2023 at 10:34 PM Ruolin He @.***> wrote:

Hi Ou,

I knew this tool is designed for high eukaryotic genomes such as plants and animals.

And I am curious whether I can use this tool in the genomes of bacteria, archaea and fungi.

Looking forward to your reply.

Best wishes, Ruolin He

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/405, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NB7YNUKRGKRIQOD663YGVLVRAVCNFSM6AAAAAA75AUPTSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAYTGNJVGE4DAOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

RuolinHe commented 7 months ago

Thank you for your response. I will try it!