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Hi,
I have come across some CNVkit output, where a gene name appears to be missing from the final calls file. Here are the two lines containing the `EGFR` gene:
```
$ grep EGFR cnvkit.called.ts…
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### If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.
#292
### Describe the goals of the changes to the analysis module.
Now that we have …
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Suggestions:
- [x] C. elegans
- [ ] E. coli
- [x] S. cerevisiae
- [ ] Plant species: http://zzdlab.com/plappisite/index.php
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Hi @kimrutherford @ValWood,
I was drafting the email to announce the changes, but I realised a few things that perhaps we should address:
* [x] A lot of "new genes" lacking references: both [pro…
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Hi
Thank you for the good tool.
I try to run the brie-count. But it returned with some error.
The code is :
`brie-count -a /data/BRIE2/AnnoSE/SE.gff3 -s /data/outs/possorted_genome_bam.bam -b …
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New CHM13 genome provides only `*.gff3.gz` files for genes annotations, see https://github.com/marbl/CHM13#v11. So we cannot configure genes markup for new genome in JBR
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Hi.
Is there a way to alter the filtering to gain more small genes? We are missing most of a whole class of genes in a plant. These genes are about 200 amino acids long. Will changing --min-coding-…
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Hi, thank you for this approach, absolutely fascinating! I'm hoping to use this in a workflow to assess and triage eukaryotic genome annotations using FoldSeek. The range of protein sequences can be s…
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Hi Tobias,
Thank you for creating the ITAG4.1 GO annotation for tomato! This is a valuable resource for the plant research community.
I am currently using your annotation to perform GO enric…
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**Describe the bug**
There is something fishy with `NM_030582.4`. Take, e.g., this deletion that maps to this transcript: [`NC_000021.8:g.46924426_46924427del`](https://variantvalidator.org/service/v…