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How to Prepare Consensus Sequences #123

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Song-10-YF opened this issue Dec 21, 2023 · 0 comments
Open

How to Prepare Consensus Sequences #123

Song-10-YF opened this issue Dec 21, 2023 · 0 comments

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@Song-10-YF
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Dear @cbergman,

Thank you for developing this analysis pipeline. I previously consulted with you on how to prepare GFF and taxonomy files. However, I have some questions regarding the preparation of consensus sequences.
After annotating with EDTA, I obtained a TElib file, which I believe to be a high-quality TE consensus fasta file. However, it includes numerous different sequences from the same TE family. As I am working with a non-model species, the identification of TEs is not entirely certain.
In this case, should I retain only one sequence per superfamily, or is it acceptable to keep multiple sequences with the same title?

Best regards.
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