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tilschaef / scRNA-seq

From fastq to preprocessed counttable (for in-house CELSeq2 method), with Kallisto | Bustools workflow.
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Parameter combined_id #21

Closed Rebecza closed 3 years ago

Rebecza commented 3 years ago

Concerns: The combined_id parameter cannot be used anymore in UMAP representations.

Did this parameter name change or is there another reason? In my latest version I am not able to label my UMAPs with setting umap_cols: anymore with the variables I combined in meta_group_id, before I could do this by using combined_id?

Rebecza commented 3 years ago

Alright, I thought I solved the issue since there was something also wrong related to my dataset specifically. But the problem still remains.

I see in my output file: phenodata.csv that a column is created in the metadata: combined_id, and this is done correctly. However, the pipeline breaks down while trying to use the combined_id for plotting onto UMAP. Because it Cannot find 'combined_id' in this Seurat object. Did something change here? Before I was able to use this parameter like this.