TE not found in the TE_SO database

Question

TE not found in the TE_SO database

Opened this issue 5 days ago · 5 comments

There are no errors in my log, but towards the end, numerous entries like SINE/tRNA-Mermaid and DNA/MULE-MuDR? are reported as not found in the TE_SO database and will therefore be excluded from renaming sequences in the final annotation. I updated the TE_Sequence_Ontology.txt to include "SINE/tRNA-Mermaid" and "DNA/MULE-MuDR?". I want to ask if this approach is correct. Will it cause any subsequent issues?

Sun Dec 22 01:51:17 PM CST 2024 Combine the high-quality TE library fugu.fasta with the EDTA library:

SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
DNA/MULE-MuDR? not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
DNA/MULE-MuDR? not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
DNA/MULE-MuDR? not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
SINE/tRNA-Mermaid not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
Sun Dec 22 01:51:42 PM CST 2024 EDTA final stage finished! You may check out:

Answer 1 · 2024-12-22T12:53:57.000Z

Thank you for your contribution to software development. Why does the generated GFF file contain "###"?

Answer 2 · 2024-12-22T13:00:52.000Z

It can be seen that there is a difference between these two tables. The final table generated by EDTA shows 0% for DNA_transposon, while RepeatMasker shows 4.1%. Could you help identify what I might have done wrong?

Answer 3 · 2024-12-22T23:34:28.000Z

Yes, you need to update TE_Sequence_Ontology.txt to include these elements that are new to the document. The ### lines separate each structurally intact TEs to better follow the GFF3 standard. You may use supply the RepeatMasker library to EDTA to enhance it's performance in detecting known TEs.

Thanks!
Shujun

Answer 4 · 2024-12-23T01:07:04.000Z

In the EDTA pipeline, we added the parameter anno -1, which caused it to run RepeatMasker and generate the results mentioned above. However, during subsequent steps, the software likely performed some integration or filtering, which resulted in the EDTA sum file. This file appears to differ significantly from the sum file generated by RepeatMasker within EDTA. What could be the reason for this? While running EDTA, we already used the --curatedlib option to include LINEs, SINEs, and TEs from the model species library.

Answer 5 · 2024-12-23T21:21:22.000Z

After homology search, EDTA will combine it with structurally intact elements, which may mask some of the homology-searched TE fragments. There is an increase of helitrons likely due to this. You may remove intact Helitrons in this file $genome.EDTA.final/$genome.EDTA.intact.gff3 to reduce the false positive introduced by the less reliable helitrons.

Shujun