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Hi,
I have used syri to obtain the structural variations between two genomes with two alignment tools (i.e. minimap2 and mummer). However, I found that most variations were different from two tools.…
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Research and discovery in
## Biology and Medicine
### Relevant Collections
- Sydney Brenner collection
- Elof Carlson collection
- Carnegie Institution of Washington at CSH administrative recor…
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**Are you using the latest release?**
Yes
If you are not using the latest release of funannotate, please upgrade, if bug persists then report here.
**Describe the bug**
A clear and concise descr…
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Hello!
We have been using the special GTF files that are supplied on the Hammell website for Transposable Elements, and have been looking at reads that were aligned with STAR. However, all of our r…
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Hi Adam,
I'm a beginner in transposable elements analysis in human genome and I'm interested in your tool TLDR. I'm wondering how do you create the teref.human.fa file (from which database or publica…
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I just had a look into the DNA-aligner snakefile for BWA and noticed that the parameter for custom BWA-arguments (alignerOpts) is not passed to the call of bwa-command: https://github.com/maxplanck-ie…
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Hello, can we use PiRATE for retrieval and annotation of transposable elements in fungal genomes, specifically Basidiomycota?
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Hi Jon!
First of all, thanks for the pipeline, it's been really useful to me!
So, I ran into this problem in predict, where it's quitting after a bedtools intersect error. From logfile:
`[09:39…
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**Are you using the latest release?**
Yep (*I think*)! Installed through Conda
```
funannotate --version
funannotate v1.8.3
```
**Describe the bug**
I ran the test set, and I got the followi…
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In the [tutorial documentation](https://funannotate.readthedocs.io/en/latest/tutorials.html#non-fungal-genomes-higher-eukaryotes) for higher eukaryotes there are a few suggestions about additional par…