Shujun Ou

@conchoecia If the repeat type is unknown to the Sequence Ontology system, then it's classified as "repetitive_sequence", a more general term that is available in the SO system. So if...

Hi Kaede, EDTA will pick up the RepeatModeler result if its final product `$genome.RM.consensi.fa` is detected. Otherwise it will run `${repeatmodeler}RepeatModeler -engine ncbi -pa $threads -database $genome.masked 2>/dev/null`, which does...

Please let me know if it works! Shujun

Maybe you want to try this parameter on RepeatModeler first to make sure it will pick up from where it stopped. You can make a copy of the unfinished run...

Hi Kaede, These files should be able to be regenerated by the indexing command: `${repeatmodeler}BuildDatabase -name $genome.masked -engine ncbi $genome.masked`; Best, Shujun

@kaede0e does it resolved?

You will need the pan-genome method to combine sublibraries to control false positives. Check out this work: https://github.com/HuffordLab/NAM-genomes/tree/master/te-annotation Shujun On Wed, Apr 6, 2022 at 9:12 AM kaede0e ***@***.***> wrote:...

Each EDTA run will have some sort of FP that can not be fully removed. Most of them are low copy. Combining multiple runs together will inflate these FP and...

Hi Xinyi, Please read the [wiki](https://github.com/oushujun/EDTA/wiki/Making-sense-of-EDTA-usage-and-outputs---Q&A) for more details. Shujun

Hi @coopergrace , Sorry for the delayed response. EDTA was using MITE-Hunter in its beta versions to identify MITEs (TIR transposons shorter than 600bp) but we found it running slowly...