The difference in LAI evaluated using the two methods is significant.

[dongaoqian]

Hello, I evaluated the LAI using results from de novo LTR identification and EDTA, but the LAI values from the two results differ significantly. I would like to know which result I should trust and why there is such a large discrepancy.

In the example below, the LAI on top comes from the de novo LTR identification result (8.83), while the LAI below is from the EDTA result (19.16). These two values differ significantly.

Here is my script：

In the following script, ”sample_v20231009.fasta.mod.pass.list“ comes from ./run_EDTA/sample_v20231009.fasta.mod.EDTA.raw/LTR/; ”sample_v20231009.fasta.mod.out“ comes from ./run_EDTA/sample_v20231009.fasta.mod.EDTA.final/

[oushujun]

You should concatenate finder and harvest scn files and give it through —inharvest. LTR_Finder_parallel produces harvest format scn files by default. Shujun

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On Wed, Sep 18, 2024 at 8:18 AM dongaoqian ***@***.***> wrote: Hello, I evaluated the LAI using results from de novo LTR identification and EDTA, but the LAI values from the two results differ significantly. I would like to know which result I should trust and why there is such a large discrepancy. In the example below, the LAI on top comes from the de novo LTR identification result (8.86), while the LAI below is from the EDTA result (19.16). These two values differ significantly. image.png (view on web) <https://github.com/user-attachments/assets/a851c0de-a4fe-4c5d-bf37-50018a2b5448> Here is my script： image.png (view on web) <https://github.com/user-attachments/assets/097fd4dc-618d-499e-b86d-05a40084ea55> In the following script, ”sample_v20231009.fasta.mod.pass.list“ comes from ./run_EDTA/sample_v20231009.fasta.mod.EDTA.raw/LTR/; ”sample_v20231009.fasta.mod.out“ comes from ./run_EDTA/sample_v20231009.fasta.mod.EDTA.final/ image.png (view on web) <https://github.com/user-attachments/assets/786f35da-c3fc-4d72-80e5-798496c04d26> — Reply to this email directly, view it on GitHub <#179>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NBCANMCZGPKHLMBGZLZXFVSHAVCNFSM6AAAAABONR22NGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZTGNJYGM2DENI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[dongaoqian]

Thank you for your reply. I reassessed the LAI using the first method, and the final result was 18.84, which differs by less than 1 from the LAI I evaluated using EDTA result.

[oushujun]

Awesome. The slight difference is acceptable. Shujun

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On Tue, Oct 8, 2024 at 9:55 PM dongaoqian ***@***.***> wrote: Thank you for your reply. I reassessed the LAI using the first method, and the final result was 18.84, which differs by less than 1 from the LAI I evaluated using EDTA result. — Reply to this email directly, view it on GitHub <#179 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NHDO2XUCGQ3NZ7SA43Z2SEHXAVCNFSM6AAAAABONR22NGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBRGEYTMNBTHE> . You are receiving this because you commented.Message ID: ***@***.***>