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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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Are those percentages or decimals for Intact and total LTR in the LAI ouputs #70

Closed linzhi2013 closed 4 years ago

linzhi2013 commented 4 years ago

Hi Shujun,

I noticed this Although LAI is independent of total LTR-RT content, estimation of LAI is empirically not accurate when total LTR-RT content is less than 5% and intact LTR-RT content is less than 0.1%

Here is the first two lines output by the LAI command:

Chr From    To  Intact  Total   raw_LAI LAI
whole_genome    1   1065919434  0.0382  0.5002  7.64    8.94

I am curious about whether the 0.0382 or 0.5002 is a percentage or just a decimal? If it is a percentage, that would mean 0.0382% < 0.1% and I should not apply LAI to my genome.

The command I used:

/nextomics/Software/Annotation/SOFTWARE//LTR_retriever/LAI \
 -genome genome.all.fasta \
 -intact genome.all.fasta.pass.list \
 -all /export/path/toRepeatMasker/result/test.out -t 20

The logs:

Fri May 22 12:16:59 CST 2020    Dependency checking: Passed!
Fri May 22 12:16:59 CST 2020    Calculation of LAI will be based on the whole genome.
                Please use the -mono parameter if your genome is a recent ployploid, for high identity between homeologues will overcorrect raw LAI scores.
Fri May 22 12:16:59 CST 2020    Estimate the identity of LTR sequences in the genome: standard mode
Fri May 22 18:50:58 CST 2020    The identity of LTR sequences: 93.5383103979807%
Fri May 22 18:50:58 CST 2020    Calculate LAI:

                        Done!

Thank you in advance!

All the best Guanliang

oushujun commented 4 years ago

Hi Guanliang,

It's in decimal. "0.0382 0.5002" means the genome has 3.82% of intact LTR-RT and 50.02% LTR sequences in total. Your command and log look good to me except the LTR identity is a bit high. Is this a polyploid species?

Best, Shujun