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zhangrengang / TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
https://doi.org/10.1093/hr/uhac017
GNU General Public License v3.0
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Insertion time calculation #45

Closed tinyfallen closed 1 year ago

tinyfallen commented 1 year ago

Dear developer,

Thanks for your great tools! Would you please add the function to calculate LTR insertion time in the package so that the user could take the convinence to finish the task all-in-one.

Best ~

2eYu commented 1 year ago

Hi @tinyfallen,

Maybe you can use EDTA to calculate LTR insertion time, but you need to add the correct parameter u(Neutral mutation rate). The default u is 1.3e-8 (per bp per year, from rice), which is not so universal for other species, so you need to calculate the neutral mutation rate(suits the species of your research) on your own.

tinyfallen commented 1 year ago

Hi @tinyfallen,

Maybe you can use EDTA to calculate LTR insertion time, but you need to add the correct parameter u(Neutral mutation rate). The default u is 1.3e-8 (per bp per year, from rice), which is not so universal for other species, so you need to calculate the neutral mutation rate(suits the species of your research) on your own.

Hi @2eYu ,

Thanks for your suggestion! I would have a try.

Best ~

zhangrengang commented 1 year ago

@tinyfallen Sorry that it is beyond the scope of TEsorter which is a classifier based on domains but has no information of LTR regions. You may try LTR_retriever or EDTA as suggested by @2eYu .

tinyfallen commented 1 year ago

Thanks a lot for your timely reply, I would take your suggestions and have a try !