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bioinformatics-core-shared-training / Bulk_RNAseq_Course_Base

https://bioinformatics-core-shared-training.github.io/Bulk_RNAseq_Course_Base/
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Packages for annotations #11

Open TomSmithCGAT opened 2 years ago

TomSmithCGAT commented 2 years ago

'Annotation and Visualisation of Differential Expression Results' explains there are multiple ways to obtain annotations and then demonstrates how to do this with AnnotationHub, which seems perfectly reasonable.

https://github.com/bioinformatics-core-shared-training/Bulk_RNAseq_Course_Base/blob/1169a4f2536ff83b69d0f748ca6d700b3406ce23/Markdowns/11_Annotation_and_Visualisation.Rmd#L57-L59

However, after this, we then load a set of annotations that was obtained via biomaRt. I assume this is a legacy issue. This is a bit confusing and I would suggest the loaded annotations should be obtained with AnnotationHub too. https://github.com/bioinformatics-core-shared-training/Bulk_RNAseq_Course_Base/blob/1169a4f2536ff83b69d0f748ca6d700b3406ce23/Markdowns/11_Annotation_and_Visualisation.Rmd#L162-L182

AshKernow commented 8 months ago

Yes, we should look at resolving this discrepancy. We no longer need the Chr, Start etc columns, just Symbol and Entrez.