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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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LAI for ployploid #83

Closed Jiny000 closed 3 years ago

Jiny000 commented 3 years ago

Hi, I used LTR retriever to calculate LAI of wheat,which is an allohexaploid(AABBDD).I took all wheat genome into LTR retriever,and I want to get LAI for each subgenome.I use this command:

for i in `subgenomeA subgenomeB subgenomeD `
do
LAI -genome wheatCS.fa -intact genome.fa.pass.list -all genome.fa.out -mono $i.list
done

The genome file ,intact file and all(.out) file are generated by whole wheat genome.The subgenomeA/B/D.list is the name list of subgenome chromosome.Can I get the correct result of LAI?Need I extract each subgenome from genome file ,intact file and all(.out) file?

Sincerely

oushujun commented 3 years ago

Yes, this is the right way to calculate LAI for polyploid. Consider using -totLTR and -iden if you want to compare multiple genomes because these two values affect LAI pretty easily. You may use values from the "best" (in a subjective manner) genome as the standard and set it on other genomes.

cassondranewman commented 2 years ago

Hello, Thank you for creating this assembly metric! I wanted to ask- if you are comparing two polyploids of the same species (an intraspecific comparison) can you simply compare the whole-genome raw LAI score?

In other words, if you are doing an intraspecific comparison of polyploids, does the corrected LAI score need to be computed per subgenome [as shown above] - or is comparing whole-genome raw LAI scores enough?

oushujun commented 2 years ago

Hi, yes, you may use raw LAI for intraspecific comparison. For polyploids, you still need to calculate LAI values for each subgenome and the comparison between same subgenomes can be done with raw LAI, but for different subgenomes, you still need to use corrected LAI.

Best, Shujun

On Sun, Aug 1, 2021 at 8:44 AM Cassondra Newman @.***> wrote:

Hello, Thank you for creating this assembly metric! I wanted to ask- if you are comparing two polyploids of the same species (an intraspecific comparison) can you simply compare the whole-genome raw LAI score?

In other words, if you are doing an intraspecific comparison of polyploids, does the corrected LAI score need to be computed per subgenome [as shown above] - or is comparing whole-genome raw LAI scores enough?

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cassondranewman commented 2 years ago

Thank you for the clarification! I appreciate it.