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Dear authors, thanks in advance for maintaining this nice and very useful software. This is not an "issue" but a couple of technical questions I have about the software.
1- How does the software d…
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Hello,
I have been trying to use TIF for a non-LTR in drosophila. I am having hard time deciding how many bp i should include in the 5' and 3' ? Also it is important to note that the 3' has…
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Hi,
I am wondering is it ok to calculate LTR insertion time using the "`identity`" from the result file `genome.mod.retriever.all.scn` ?
Bests,
Tao
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Hi Shujun,
It seems that EDTA does not specifically identify LINE/SINE since EDTA_raw.pl only finds ltr|tir|helitron. Has it been benchmarked in animal genomes (e.g. human) where these elements ar…
hkchi updated
4 years ago
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I am trying to run LTR_retriever from the ltr_finder results using the following scripts:
ltr_finder -D 15000 -d 1000 -L 7000 -l 100 \-p 20 -C -M 0.9 /home/icar/Jute_genomes/ltr_finder/LLWS01.1.fa …
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**What is this request referring to?**
#487
Parent | labels | Synonyms | about
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SO:0000186 | LTR/Copia | RLC, Ty1, Copia, LTR-Copia | LTR retrotransposon in the Copia superfami…
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The LARD and TRIM retrotransposons are found in many eukaryotes, and were described about 15 years ago. These elements have been shown to be involved in a number of important phenotypes and I propose …
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Hi Hwan,
Thanks for this nice tool! I want to try it on my RNA-seq data but the species (Rhesus) is not included in Repbase. So I want to create a `FASTA` file for `SalmonTE`.
I've seen this tut…
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I seek help in a few different areas, by way of your response to this post. Some context first - Here are my LTR discovery goals. For my genome of interest, I want to report the following:
Type 1. **…
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Hello,
I am running LTR_retriever on a new accession of the grass Brachypodium. (I ran LTRHarvest on the masked genome because I want to identify novel LTR-RTs that aren't in RepBase.) I have run L…