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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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EDTA annotation step #247

Closed elissaralam closed 2 years ago

elissaralam commented 2 years ago

Hello,

I ran EDTA on a contig assembly and obtained a repeat library. I would like to annotate the scaffolded version of the same assembly with that repeat library. Based on your code commentary, I can ask EDTA to only annotate a provided genome by specifying --step anno. But I am unsure how to provide the custom library with which I want EDTA to annotate the provided genome. I would appreciate your guidance. Just to clarify, my aim is not to mask the genome. I want to annotate the scaffolded genome with repeats because i would like to perform repeat density analysis in a downstream step.

Thanks, Elissar

oushujun commented 2 years ago

Hi Elissar,

Sorry I missed your issue somehow. If you want to perform a full annotation on your scaffolded genome you will need to rerun EDTA. If you want to perform a homology annotation with the library generated from contigs, you can use Repeatmasker with -lib as the EDTA generated library (lib.fa).

Best, Shujun