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waldronlab / SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets
https://bioconductor.org/packages/SingleCellMultiModal
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celltype metadata in scMultiome 10x PBMC tutorial #50

Closed akhst7 closed 1 year ago

akhst7 commented 1 year ago

Hi,

In the scMultiome 10x PBMC tutorial tutorial section under a heading Cell Metadata,
celltype: The cell types have been annotated by the 10x Genomics R&D team using gene markers. They provide a rough characterisation of the cell type diversity, but keep in mind that they are not ground truth labels.

Which file the output of a 10x sample data (see below) set contains this cell type metadata in the output of a 10x sample data set ?

Screenshot 2023-03-01 at 4 16 24 PM

LiNk-NY commented 1 year ago

Good question. Perhaps @aljabadi or @rargelaguet can answer this.

drighelli commented 1 year ago

Dear @akhst7,

I'm sorry for the late answer, we looked into that and can now give you an answer.

The annotation was manually curated by a 10x Genomics team and it is not available in Ricard's script nor in the output of cellranger.

Generally speaking, AFAIK cellranger is not able to assign cell types, so you'll never find this information in its standard output.

By the way, you can find the celltype annotations for this specific dataset in the colData of the MultiAssayExperiment returned by the scMultiome function of our SingleCellMultiModal package.

I hope this answer could be useful.

Dario