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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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Any possibility to use output of repeatmodeler for LAI evaluation? #103

Closed ghost closed 2 years ago

ghost commented 2 years ago

Hi,

I am working on a maize genome. After assembly and scaffolding, I used repeatmodeler to generate a repeat library with argument "---LTRStruct". The output contains LTR sequence annotation. For LTR_retriever, is there any possibility to feed it with output from repeatmodeler or repeatmasker for the LAI calculation? Otherwise, I need to rerun LTRharvest by myself although repeatmodeler already employed LTR_retriever for its task.

Many thanks in advance.

Best, Meiyuan

oushujun commented 2 years ago

No, you need to run LTRharvest and LTR_FINDER for LAI. Using only LTRharvest results will have lower LAI.

Shujun

On Wed, Jul 28, 2021 at 3:16 PM MeiyuanJi @.***> wrote:

Hi,

I am working on a maize genome. After assembly and scaffolding, I used repeatmodeler to generate a repeat library with argument "---LTRStruct". The output contains LTR sequence annotation. For LTR_retriever, is there any possibility to feed it with output from repeatmodeler or repeatmasker for the LAI calculation? Otherwise, I need to rerun LTRharvest by myself although repeatmodeler already employed LTR_retriever for its task.

Many thanks in advance.

Best, Meiyuan

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