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I would like to use the pipeline on a large plant genome. Would it be to run separately on chromosomes or directly on the entire genome? Are there any requirements for CPUs and RAM? Have you ever test…
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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` …
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### Description of the bug
Running the pipeline on "real" data returns an error, with the log showing the cause as a missing file (`test.fa`). Creating this file in the current/working directory (e.g…
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Hi there,
I am using `bambu 3.4.0` for quantification. I am curious about the read to transcript assignment, so I used the function mentioned in the document `metadata(se)$readToTranscriptMaps[[1…
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Hi,
I am working on annotating large datasets, specifically Whole Genome Sequencing (WGS) VCF files, using the Variant Effect Predictor (VEP). However, the annotation process is taking significantl…
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I tested these two links, and they worked as expected.
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=6060535&retmote=rsr
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esear…
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### Operating System
Ubuntu 22.04
### Other Linux
_No response_
### Workflow Version
v1.4.0
### Workflow Execution
Command line (Cluster)
### Other workflow execution
_No re…
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Hello !,
I want to use TOGA for genome annotation and I downloaded the reference genome, but the problem is is that more than 50% of the CDS are not the multiples of 3.
Can you please guide me in t…
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Thank you for the best software for TE annotation. I use the RepeatModeler for one larger genome TE annotation, and find produce a few of files for rmblast alignment. I check the code ,and find the …
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Could you please explain how to download annotation reports in *.jsonl format for a single organism or multiple organisms of a particular taxid using datasets?
The `dataformat` seems to have a comm…