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Hi, I am running the Scenic+plus pipeline with Zebra fish and I am getting `Unable to load annotation for custom` warnings when I run `run_pycistarget`
All databases created specifically for Zebra …
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Thanks for developing this great tool and make it available!
I was wondering if it is possible to use other methods of gene calling and annotation besides Anvio. Looking at the required input files…
juanu updated
4 months ago
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I met an error like this when I try to update me annotation using Launch_PASA_pipeline.pl, please help me fix it or give me some advice.
* [Fri Sep 15 01:56:05 2023] Running CMD: /home/MCY/App/PASApi…
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I am running the long reads xTea and I am having an issue when running HG38. This was not an issue using T2T reference.
When I am running HG38 with the below command, everything runs smoothly until …
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example: https://pubmed.ncbi.nlm.nih.gov/37081487/
[pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls]( https://pubmed.ncbi.nlm.nih.gov/37081487/)
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The aim is to be able to obtain the full transcript sequence in case of unannotated intron retention events. Following the StringTie workflow, this would mean considering retained introns (which have …
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When I tired to use CreateModelEggNogPool.carveme_pipeline("Scer", "Saccharomyces_cerevisiae_S288C_GCF_000146045.2","data/annotations/functional/example.fasta.emapper.annotations","data/annotations/fa…
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### Description of feature
Currently, the `.cnn`, `.cns`, and `.cnr` gene columns are not annotated by default as the `cnvkit/batch` module is missing the annotate argument.
```
chromosome star…
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Hi,
Now I want to incorporate RNA-seq via PASA when conducting the genomic gene annotation. When I used the FastQC for assessing my Illumina RNA-seq data, I found there were many overrepresented seq…
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FLybase and SGD have more complex multi-term phenotypes that require special consideration in the modeling.
We need to plan and implement ingests for these.