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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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CACTA #385

Closed bijendrabio closed 9 months ago

bijendrabio commented 9 months ago

Hello, EDTA appears to underestimate CACTA content. Could you please kindly confirm it its true @oushujun

Regards, B

oushujun commented 9 months ago

Dear B,

I don't have such an impression. Can you show some observations?

Shujun

On Fri, Sep 8, 2023 at 5:33 PM bijendrabio @.***> wrote:

Hello, EDTA appears to underestimate CACTA content. Could you please kindly confirm it its true @oushujun https://github.com/oushujun

Regards, B

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/385, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NCDAHUCER5IDJJMV7LXZOFI7ANCNFSM6AAAAAA4Q5Q6PE . You are receiving this because you were mentioned.Message ID: @.***>

oushujun commented 9 months ago

Close due to no response. Please reopen if you have more questions or need any help.

bijendrabio commented 8 months ago

Dear B, I don't have such an impression. Can you show some observations? Shujun … On Fri, Sep 8, 2023 at 5:33 PM bijendrabio @.> wrote: Hello, EDTA appears to underestimate CACTA content. Could you please kindly confirm it its true @oushujun https://github.com/oushujun Regards, B — Reply to this email directly, view it on GitHub <#385>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NCDAHUCER5IDJJMV7LXZOFI7ANCNFSM6AAAAAA4Q5Q6PE . You are receiving this because you were mentioned.Message ID: @.>

@oushujun Apologies for the delayed response. I recently conducted an EDTA analysis on the wheat B subgenome, and the results revealed a CACTA composition of merely 3%.

TIR -- -- --
CACTA 300127 167907699 3.26% Mutator 185881 74630333 1.45% PIF_Harbinger 104108 50221788 0.97%

This results, however, contrasts with most published studies, which consistently report CACTA compositions ranging between 10% and 20%.

Kindly suggest. B

oushujun commented 8 months ago

It's hard to know which one is "correct" and neither can be wrong given the state of genome annotation. It can be frustrating if you consider the published number as "correct". To find out, you can evaluate the annotation consistency using EDTA/util/evaluation.pl to find out which version of annotation is more consistent, but this still won't tell you which one is more "correct" without manual curation.

Shujun