Closed xinshuaiqi closed 5 years ago
Hi Xinshuai,
The line you were suggesting in the ReadMe
is just an example to run LTR_retriever
. Please refer to the full usage in the manual pdf. It is still recommended to use both LTRharvest
and LTR_finder
as raw input to improve the LTR library sensitivity (marginally, though, please refer to the supplementary table for this margin) for the purpose of whole-genome LTR annotation. For the use of LAI, it is strongly recommended to use both inputs to fully identify intact LTR-RTs, otherwise the resulting LAI could drop a couple points.
Shujun
Hi Shujun, I notice the updated Readme file now suggest using "LTRharvest" as input file. Are there any reason LTR_finder no longer preferred? Is the result based on solo LTRharvest robust enough?