LTR classfication in pangenome pipeline

[jia-wu-feng]

Dear shujun,

Thanks for your great software!

When I used the pangenome pipeline of EDTA, the ratio of LTR Copia and LTR unknown changed.

Is it possible to add related species to the pan-genome pipeline?

We have a genome not of the same species, but of closely related species. However, it is also closely related species that undergo large changes in LTR annotation.

I would like to know your views on the use of the EDTA pangenome pipeline between different species.

Thanks, Jiawu Feng

[oushujun]

Hi Jiawu,

Can you please describe your inputs, commands, and parameters?

Shujun

On Mon, Oct 10, 2022 at 5:22 AM jia-wu-feng @.***> wrote:

Dear shujun,

Thanks for your great software!

When I used the pangenome pipeline of EDTA, the ratio of LTR Copia and LTR unknown changed.

Is it possible to add related species to the pan-genome pipeline?

We have a genome not of the same species, but of closely related species. However, it is also closely related species that undergo large changes in LTR annotation.

[image: image] https://user-images.githubusercontent.com/24247803/194834206-bb331496-6b6e-4873-acc8-edf3b287293c.png

I would like to know your views on the use of the EDTA pangenome pipeline between different species.

Thanks, Jiawu Feng

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/303, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NGD4X6R2IST5GGPBMLWCPN4XANCNFSM6AAAAAARBFA554 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[jia-wu-feng]

EDTA.pl --genome genome.fa -t 50 --anno 1

I did not use the TE lib, so I use genome.mod.EDTA.TElib.fa for pangenome.

Thanks, Jiawu

[oushujun]

I don't follow what you mean. How many genomes do you have?

On Tue, Oct 18, 2022 at 5:06 AM jia-wu-feng @.***> wrote:

EDTA.pl --genome genome.fa -t 50 --anno 1

I did not use the TE lib, so I use genome.mod.EDTA.TElib.fa for pangenome.

Thanks, Jiawu

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[jia-wu-feng]

I have 19 genomes, one is specie 1, and 18 are specie 2. I want to analyze the 2 species' TE differences.

When I used EDTA normal pipeline and pangenome pipeline, the specie 1 in LTR has a lot of change.

[oushujun]

Thank you for the extra information. It could be that some families are border-line classified and the rerun (panEDTA) have it classified as unknown. You may rerun panEDTA to regenerate the panTE library or use TEsorter with REXDB-plant to reclassify the panTE library and see if there's any improvement.

Shujun

On Tue, Oct 25, 2022 at 10:27 AM jia-wu-feng @.***> wrote:

I have 19 genomes, one is specie 1, and 18 are specie 2. I want to analyze the 2 species' TE differences.

When I used EDTA normal pipeline and pangenome pipeline, the specie 1 in LTR has a lot of change.

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/303#issuecomment-1290646716, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NE2LWAIUWZDYWMAJYDWE7U65ANCNFSM6AAAAAARBFA554 . You are receiving this because you commented.Message ID: @.***>

[oushujun]

Any updates?

[oushujun]

Close due to no update. Please reopen if you still have questions. Thanks!

Shujun