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Just wanted to know if there was a way to specify the hg38 reference genome for the `CNV.create_anno` step, I couldn't find any arguments that allow this but I could have missed something. Thank you!
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Match GDC
- hg38
- v36
[ref](https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files)
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### Current Behavior
Currently, the tool uses the hg38 endpoint for annotations, and all annotations are thus based on the hg38 build.
### Proposed Solution
- Investigate and confirm the curr…
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### Description of the bug
recently I tried to help a user to run the nf-core/circRNA pipeline, but met tons of errors. And this is one of the latest after I downloaded the reference genome from aw…
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Hi @olearyna,
I was using the field `annotation_info` from `genome/accession/{accession}/dataset_report` to tell users whether a given assembly has annotations. Since yesterday, it seems that `anno…
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Dear AmpliconSuite Developers,
First of all, thank you for developing such a great software that provides a lot of convenience for ecDNA research. I encountered a little difficulty when trying to a…
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Hi @tomasbruna,
I ran Braker to predict gene structure and got the problem in the step running Genmark-EX as below.
I used the reference genome and customized amino acid sequence database with t…
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Hi,
I tried to quantify the intron rentention level for a transposon gene and manually made a genome file and a gtf file.
IGV visualization of the bam files in the tmp folder shows clear difference …
circR updated
2 weeks ago
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@donovan-h-parks,
First off: The Prokaryotic Genome Annotation Pipeline (PGAP) uses CheckM to evaluate the completeness of hundreds of thousands of assemblies. Our use of CheckM has directly improv…
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Currently, `seqinfo` is empty. It should be populated based on the genome we use.
Is there a way to store the annotation (ie. gencode) inside the object? Not sure how, perhaps look at the `txmeta` …