-
Hello, I have encountered the following problems when using the software, can you help me to see where the problem is? thank you
##########################
### LTR_retriever v2.9.1 ###
##########…
-
Hi shujun,
I tried to run LTR_retriever, but I met an error like below.
##########################
### LTR_retriever v2.9.6 ###
##########################
Contributors: Shujun Ou, Ning Ji…
-
When I run the LTR_retriever : `/software/LTR_retriever-2.9.5/LTR_retriever -genome N02.fa -inharvest N02.fa.rawLTR.scn -threads 10 -u 7.3e-9`, I receive some warning information:
1. awk: cannot o…
-
Dear Immortal2333,
I am using your method to identify centromeres.I find that there is a aligned area where Copia ,Gypsy ,Helitron are blank in each chromosome in your plot,which is the centromere ar…
-
Hi,shujun
I am running the LAI index on a newly assembled genome (less than 200Mb). The contiguity is pretty good with N50>1.2Mb.
I have the following results :
Chr From To Intact Tota…
-
Dear @zhangrengang
TEsorter is a very good tool that we used in our recent research.
Our recent study may wish to identify collinearity (synteny) of LTRs across species (although it's not clear…
-
Hi @zhangrengang
The species I am studying (a kind of Rhododendron) does not have a reference genome. Now I want to know how to analyze the effect of transposons ((mainly LTR retrotransposons) on…
-
After using LTR-FINDER to get ocu.finder.scn, run LTR_retriever.
LTR_retriever -threads 10 -genome new.genome.fasta -infinder ocu.finder.scn.
But I get the title error: ERROR: No candidate …
-
I am having a similar problem as a few other users hee, but can't solve it.
I'm working with the following tools within a conda environment
- bedtools v2.30.0
- samtools 1.17
- R version 4.2.2…
-
Hi Shu Jun, I have a question that needs your answer. I used Repeatmodeler and RepeatMasker to perform de Novo and homology annotation on the genome, but I found that the LTR in the obtained result wa…