Hi Allen Community,
I am trying to obtain the celltype information regarding the clusters or cells in the WHB 10x RNA-seq data that I obtained from the ABC atlas. The data files only consist the expression matrix and the regular metadata. I noticed that there are tutorial on using the taxonomy files to annotate the clusters. Is that the right and only way to obtain the celltype information or there are a easier way? Thank you!
Hi @aliceZ
We intentionally kept the metadata in the .h5ad files to a minimum. Our thinking was: cell type annotations may change over time (or evolve as our understanding of cell types evolves), but “this cell came from this donor and this is its gene expression vector” almost certainly will not. Cell type annotations and other more “subjective” metadata is stored in separate CSV tables that can be downloaded through our data access tool.
This notebook (which is presumably what you were referring to) shows how to access the cell type annotations and associate them with the gene expression data. It is, as you say, the only officially sanctioned way to access those annotations.
Please let us know if anything is unclear or difficult to use.