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Hello,
I’m very excited to use TEtranscripts. However, I work with a non-model genome, and there are no gene and TE annotation files available on your website for this species. Would it be possible…
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We have encountered an issue related to the use of GTF and FASTA files during our analysis. The official examples provided in your documentation use gencode.v26lift37.annotation.gtf.gz and ucsc.hg19.f…
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Hi Prof. Ou,
First, EDTA v2.2.0 was used for TE annotation of the NO1 genome assembled with HiFi reads.
Then, we calculated the LAI value using the LTR annotation results (LAI software …
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### Description of feature
Hi Jason,
This workflow looks great and I hope to try it out soon.
If you haven't already considered it, you might want to take a look at incorporating this tool as an a…
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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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```
### Pipeline run code and environment:
* Command: `/my/path/pepatac/pipelines/pepatac.py -O /my/path/OUTPUT -P 10 --sample-name sample_S1_R1_001 --input /my/path/FastQ/sample_S1_…
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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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### 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
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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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…