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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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Too many 0 LAI values #122

Closed Wenwen012345 closed 2 years ago

Wenwen012345 commented 2 years ago

Hello, @oushujun

Most LAI values of individual species generated by using the LTR-retriever run are clustered at 0. What is the problem? Is it a very small number of transposons, or is it a sequencing problem, or what?

Here are the software parameters:

LTRharvest
gt suffixerator \
  -db 1.fa \
  -indexname 1 \
  -tis -suf -lcp -des -ssp -sds -dna
gt ltrharvest \
  -index 1 \
  -similar 90 -vic 10 -seed 20 -seqids yes \
  -minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6 \
  -motif TGCA -motifmis 1  > 1.scn &
 LTR_FINDER
ltr_finder -D 15000 -d 1000 -L 7000 -l 100 -p 20 -C -M 0.9 1.fa > 1.scn &

LTR_retriever -genome 1.fa -inharvest 1.harvest.scn -infinder 1.finder.scn

The species are Rhododendron williamsianum and Rhododendron simsii. The assembly link is:

  1. https://www.ncbi.nlm.nih.gov/assembly/GCA_009746105.1/
  2. https://www.ncbi.nlm.nih.gov/assembly/GCA_014282245.1/

LAI distribution pictures are as follows: https://weibo.com/2215415680/Lp043sOxg

So that's Question 1

Question 2 is whether the following LAI distributions are also normal? It seems that there are too many 0 values: https://weibo.com/2215415680/Lp21UyZUV

I was led here to ask questions.

That should be the last question. ^s^ Thank you so much!

oushujun commented 2 years ago

Hello @wensulin93,

If you can run LAI without errors, that means the program is performing as expected. If you get 0 LAI value for your genome, it suggest the repeat assembly of this genome is not good. The interpretation also applies to reigonal LAI values.

Best, Shujun