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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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A reviewer's comment related to the setting of mutaion rate #164

Closed zhdang closed 2 months ago

zhdang commented 3 months ago

Dear Shujun,

We utilized the LTR_retriever to estimate the insertion time of LTR-RTs in our studied genome and other reference genomes. Regarding the analysis, the reviewers have raised a concern: "The mutation rates of the selected species are different. How are the mutation rates for these species set in the analysis of LTR insertion times?" Would you please suggest to us how we should address or respond to this issue? You mentioned setting the mutation rate using the parameter -miu in a previous issue. Is the mutation rate for specific species included in the results of the LTR_retriever analysis? Do we need to set the -miu parameter when analyzing specific species, or is it ok to use the same default parameters?

Looking forward to your reply.

Best regards, Zhenhua Dang

PS: Our analysis is shown below; the red line represents our studied species. We mentioned a 0.3 million years ago (mya) insertion of LTR-RTs in the genome. The LAI of the genome is 13.1.

LTR LTR Assembly Index

oushujun commented 3 months ago

Yes, the default mutation rate is from rice. You may specify a mutation rate of your species to be more accurate.

Thanks, Shujun

zhdang commented 3 months ago

Hi Shujun, Thank you very much for your reply, I will try this. Cheers, Zhenhua

发件人：Shujun Ou @.> 发送时间：2024年3月15日(星期五) 03:08 @.> @.>; @.> 主　题：Re: [oushujun/LTR_retriever] A reviewer's comment related to the setting of mutaion rate (Issue #164) Yes, the default mutation rate is from rice. You may specify a mutation rate of your species to be more accurate. Thanks, Shujun — Reply to this email directly, view it on GitHub <https://github.com/oushujun/LTR_retriever/issues/164#issuecomment-1998181507 >, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALSTT5XTAJV67NJWIS7J5U3YYHYS7AVCNFSM6AAAAABERLH37CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJYGE4DCNJQG4 >. You are receiving this because you authored the thread.Message ID: @.***>