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A novel transcript (**ENST00000484532**) is not appearing in the output of my local VEP (v108) or the current Ensembl UI. Could this be due to a pre-filtration step, or are certain transcripts intenti…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
What are the collection types and names? Example:
- Arachis/stenosperma/annotations/V10309.gnm1…
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### Description of the bug
I'm having some trouble getting the `test` data to run via `singularity` with `alevin`, specifically if I supply my own genome/annotation. It's failing at `SIMPLEAF_INDEX`
…
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**Describe the bug**
I lifted annotations from a reference genome to another isolate with LiftOff. I wanted to check how the new annotations are. Do they have start and stop codons or in-frame/premat…
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### Description of the bug
When I use my custom reference, error always show: This path is not available within annotation-cache. Please check https://annotation-cache.github.io/ to create a request …
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Dear Bambu team,
I am running a massive project with 480 BAM files with ~4.8 TB total data.
Following the previous suggestion for Bambu, I am running first the extended annotations (`quant = FALSE…
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CP072753.1 RepeatMasker similarity 1 77 2.7 + . Target "Motif:(AACCCT)n" 1 76
CP072753.1 RepeatMasker similarity 4121 4244 0.0 + .…
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Hello Team!
I built a reusable sub workflow for performing BUSCO on genome alone, or on genome and annotation. I have used it in two other pipelines. It is currently sitting in my own modules repo: …
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Hi,
thank you for this great tool.
I am running spacemake for an openST data and encountering the following Error when running `spacemake run --cores 8`:
```Error
KeyError in line 286 of /ho…
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Hello,
I encountered the following error during the execution of my circular RNA analysis pipeline:
```bash
Indexing .bam file...
open: No such file or directory
[bam_index_build2] fail to op…