Generating trained model

[jdaron]

Hello,

I am interested in using TEforest with my own genome. I would like to ask whether it is necessary to generate a new trained model, or if I can use one of the models that are already provided.

Thanks,
Josquin

[austintdaigle]

Hi Josquin,
Thanks for your interest in TEforest. In principle, TEforest is designed to detect TEs in any species, though our current models are only trained using Drosophila insertions. For the revision of our paper, I have been working on a newer set of models that are more robust than the current models for this task, which I should be able to release in the coming weeks. I'll also be improving the documentation and input file structure to make it easier to use. I have currently had success testing TEforest on Drosophila datasets, humans, and C. elegans. It is unclear how the model will behave when used on much more repetitive genomes (Ex plants, Aedes mosquitoes, etc). If you have any problems using TEforest or find any performance issues in your species let me know, I am happy to help and improve the tool.

Austin

[jdaron]

Hi Austin,
Thanks for the feedback I am about to use your program, I will let you know how it goes. I am actually working on Aedes mosquitoes and I will be interested of working with Aedes models if you have them.
Josquin