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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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Differences between LTR-retriever and RepeatMasker #53

Closed xiaenhua closed 4 years ago

xiaenhua commented 4 years ago

Dear Shujun, Thanks for developing LTR_retriever. I used LTR_retriever to annotate a subset sequences of a plant genome and found 2333 intact LTR-RTs. This number is much less than that annotated by RepeatMasker (approximate 11743 ) with non-redundant LTR-RTs reported by LTR_retriever. How to explain such differences? Which datasets should I use for downstream analysis? BTW, I only focus on the evolution of LTR-RTs.

With kind regards,

Enhua

oushujun commented 4 years ago

Dear Enhua,

I forgot if I have replied to your question or not. Sorry if I missed it. LTR_retriever identifies intact LTR retrotransposons, which usually a small fraction of all LTR sequences (intact, solo LTR, truncated, fragmented, remnants, LTR-like...) that are annotated by RepeatMasker. The two datasets represent different aspects of a genome and using which depends on your analysis. Hope this helps!

Best, Shujun