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Dear Kevin,
Greetings!
In the follwoing environment;
conda activate transposon_annotation_reasonaTE
reasonaTE -mode pipeline -projectFolder workspace -projectName testProject
I got the follo…
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Dear Jiangzhao
Thank you and your team for developing this excellent software, which is obviously very useful and relieves researchers from the huge workload of manual curation.
I successfully r…
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Hi! Thanks for the excellent tools!
How can I get the annotation of specified TE type (e.g. LTR or TIR)? Like the "Divide and conquer" part in EDTA pipeline. Many thanks!
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- reference is http://www.ncbi.nlm.nih.gov/pubmed/21523651
- 4414-bp element, non-autonomous LTR element
- related to D. yakuba Pifo_I: http://www.girinst.org/protected/repbase_extract.php?access=Pifo…
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For example, using a comparison between two datasets (e.g. two different genetic backgrounds) we can get an overview which genes have a large difference in the number of transposon insertions and/or r…
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Hi
I was running `RepeatModeler - 2.0.1` for my genome TE annotation, still return a high proportion `Unclassified` (33.39 %, 53% in total). I have checked the RepBase according to #128. But nothing …
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Hi,
That is a very nice and smart tool, I like this tool,But in running this tool, I have some doubts.
When repeatmodeler + repeatmasker and earlgrey were used respectively on the same genome, earl…
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For estimating the fitness level for each insertion, the data needs to be normalized to compensate for the fact that the likelihood for transposon insertions is not constant throughout the chromosomes…
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Hi!
Thanks for developing dante_ltr. I tried to run dante and dante_ltr on a genome but received an error message during the dante_ltr step.
I ran dante and dante_ltr with the following commands…
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I have three questions for using IM-fusion:
1. Your article identify TE insertions from RNA-Seq based on Sleeping Beauty (SB) transposon model. But, I have several RNA-Seq data sets from Normal vs …