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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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Intact LTR elements are identified less than expected #67

Closed oushujun closed 4 years ago

oushujun commented 4 years ago

Dear Dr.ou,

So sorry to trouble you. We predicted LTR of C.sativa ,C.capsularis and G.raimondii using LTR_finder( -D 15000 -d 1000 -L 7000 -l 100 -p 20 -C -M 0.85) and LTRharvest (-similar 75 -seed 20 -minlenltr 100 -maxlenltr 7000 -maxdistltr 20000 -mintsd 5 -maxtsd 6 ). Then we retrivered LTR from the the result above by LTR_retriver. However, we obtained a small number of LTR, range from 1362 to 2145. We can't find any resons for that anyway, would you like to give us some suggestions?

_Originally posted by @chenjunhui in https://github.com/oushujun/LTR_retriever/issues/55#issuecomment-616282136_

oushujun commented 4 years ago

Hi @chenjunhui,

I assume the LTR numbers you referenced are intact LTR elements listed in the *.pass.list file. For fragmented LTR sequences, you may use the *LTRlib.fa library to repeatmask the genome.

The number of identifiable intact LTR elements is dependent on the quality of genome assembly especially on the TE space. Please refer to our LAI paper regarding the LTR Assembly Index for more details. For your information, the LTR scan I run on the G.raimondii_JGI_221_v2.0 genome (Illumina-based) a while ago only returned 1672 intact LTR elements, which is likely due to it's low-quality TE space assembly.

Hope this helps!

Shujun