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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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LAI #387

Closed Xinxin0314 closed 9 months ago

Xinxin0314 commented 9 months ago

Hi，

I found I met a question that I can't analysis the LAI result.

First, I used the EDTA to identify the TE. Then I used the command "LAI -t 10 -genome /md1200/genome.v1.fa -intact ~/genome.v1.fa.mod.EDTA.raw/LTR/genome.v1.fa.mod.list -all ~/genome.v1.fa.mod.EDTA.final/genome.v1.fa.mod.out &> lai.out &" to calculate the LAI. I got two result files: genome.v1.fa.mod.out, genome.v1.fa.mod.out.LAI.LTR.ava.age and genome.v1.fa.mod.out.LAI.LTR.ava.out, and, lai.out was empty. While genome.v1.fa.mod.out.LAI.LTR.ava.age only have one line, the content is "Input:zdd0006.genome.v1.fa.mod.out Seq_num:207806 Mean_identity:94.7854070084853". And another file had large contents.

I would like to know from which file I could obtain LAI values for assessing genome quality.

Thank you~ Looking forward to your reply.

Best wishes, Xin

oushujun commented 9 months ago

H Xin,

you used the wrong files for -intact and -all. please check out the relevant issues.

shujun

On Tue, Sep 19, 2023, 3:59 AM Xoey @.***> wrote:

Hi，

I found I met a question that I can't analysis the LAI result.

First, I used the EDTA to identify the TE. Then I used the command "LAI -t 10 -genome /md1200/genome.v1.fa -intact ~/genome.v1.fa.mod.EDTA.raw/LTR/genome.v1.fa.mod.list -all ~/genome.v1.fa.mod.EDTA.final/genome.v1.fa.mod.out &> lai.out &" to calculate the LAI. I got two result files: genome.v1.fa.mod.out, genome.v1.fa.mod.out.LAI.LTR.ava.age and genome.v1.fa.mod.out.LAI.LTR.ava.out, and, lai.out was empty. While genome.v1.fa.mod.out.LAI.LTR.ava.age only have one line, the content is "Input:zdd0006.genome.v1.fa.mod.out Seq_num:207806 Mean_identity:94.7854070084853". And another file had large contents.

I would like to know from which file I could obtain LAI values for assessing genome quality.

Thank you~ Looking forward to your reply.

Best wishes, Xin

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Xinxin0314 commented 9 months ago

Hi shujun，

Thank you for reminding me. I solved the problem.

Best wishes, Xin