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1) i want runin te for non-human wgs
2) how should i prepare the library for xTea
3) i mean how to prepare the format of library than xTea need, ps, repeatmasker output format -> xTea library format…
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Dear @quanc1989
Thanks your share about this useful and detailed analyses pipeline. I have a question about Log2 foldchange (LFC) of enrichment analysis for repeat elements intersected with breakpoi…
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Hi Ren-Gang,
There are about 88 SINE families reported by this [study](https://academic.oup.com/plphys/advance-article/doi/10.1093/plphys/kiab524/6430992). They have included HMMs for these [famili…
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Hello @clemgoub,
I ran dnaPipeTE for my samples. At the end of each run, I have fasta sequences in Trinity.fasta, along with a summary of repeat families listed in ".tbl" output files. However, non…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/functionalgenomics/UCSCRepeatMasker
Confirm the f…
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**What do you want to know?**
**Helpful context**
* Is there a particular genome assembly or organism your question is about? If possible, please provide a link to a publicly available assembly …
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I have tried install grids both using conda and git clone https://github.com/PapenfussLab/gridss.git, however, grids stools file to be installed it seems. Any suggestions?
./virusbreakend --k…
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Hi, I am trying to include a custom repeat library generated with RepeatModeler into my repeat classification with RepeatMasker-4.1.2.
In older versions of RepeatMasker, one could use the query sc…
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Dear authors,
I am trying to use Braker on RNA-seq data, and I have a question about your recommendation to use a softmasked genome.
In your tutorial for Augustus (https://github.com/Gaius-Augus…