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Question on species choice for --curatedlib parameter #546

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sanyalab opened this issue Feb 27, 2025 · 0 comments
Closed

Question on species choice for --curatedlib parameter #546

sanyalab opened this issue Feb 27, 2025 · 0 comments

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@sanyalab
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sanyalab commented Feb 27, 2025

Hello @oushujun

I am annotating a grass species, that belongs to the Poales order. It is the first in its clade to be sequenced and annotated, therefore has no fully sequenced and annotated sister species. In cases like these, can i use the curated sequences from model species in Poales (maize, sorghum, etc) to give to the --curatedlib parameter? Do I have to tweak any parameters in EDTA in order to maximize the 80-80-60 rule? I ask since most repeat elements will probably be novel, therefore structure based repeat finder LTRDigest and others will be more active in describing them.

Thanks
Abhijit

@sanyalab sanyalab closed this as completed Mar 6, 2025
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