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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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Benefit of using panEDTA #428

Closed Isoris closed 4 months ago

Isoris commented 4 months ago

Hello, I would like to compare the TE landscapes of different species of the same taxonomic order. I have obtained the TE libraries using EDTA for each species. Now if I use panEDTA and reannotate each species using the panTE library, will the TE landscape be of higher quality? What are the advantages of using panEDTA over EDTA multiple times?

Can I be able to find which TE are present in a subset of species or common to a subset of species but not in others? Which are present and absent ?

Can I compare two repeat landscapes of two species by using EDTA two times? Or should I only compare them if I have used panEDTA?

Thank you for your answer because I don't really understand what type of analysis that panEDTA allow over EDTA for between species and not within species analyses?

oushujun commented 4 months ago

PanEDTA gives you higher quality annotations and consistent names so that you can compare across genomes.

Shujun

On Sun, Feb 4, 2024 at 4:07 AM Quentin Andres @.***> wrote:

Hello, I would like to compare the TE landscapes of different species of the same taxonomic order. I have obtained the TE libraries using EDTA for each species.

Now if I use panEDTA and reannotate each species using the panTE library, will the TE landscape be of higher quality? What are the advantages of using panEDTA over EDTA multiple times?

Can I be able to find which TE are present in a subset of species or common to a subset of species but not in others? Which are present and absent ?

Can I compare two repeat landscapes of two species by using EDTA two times? Or should I only compare them if I have used panEDTA?

Thank you for your answer because I don't really understand what type of analysis that panEDTA allow over EDTA?

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