Closed akhst7 closed 1 year ago
Good question. Perhaps @aljabadi or @rargelaguet can answer this.
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
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 ?