Map cells to their cell type

Hi everyone!

I have downloaded the [WMB-10Xv2] expression matrices and also matched them to their corresponding meta data mathcing by cell barcodes in the obs table of h5ad file and csv file of metadata.

The last column of metadata table is cluster_alias and I was presuming that each id in this column can be matched to one of the ~5200(updated to 5322) clusters defined for mouse brain clusters defined in [Yao et. al].
So, the cells could be mathced to their clusters, classes, sub-classes with different levels of granuality using cluster_alias as the mathcing id.
while merging two tables (cell_meta_data and ‘cluster_annotatin’ sheet of this xlsx file), I noticed that the cluster_alias column does not include values ranging from 1 to ~5200 but has some values arouund 14000!
Accordingly, I’m posting this here to ask how can I map each cell of each of WMB-10X databaes to its cell type with different levels of granuality?

@jeremyinseattle @tylermo
Thanks in advance

Hey Mostafa,

It looks like the column you want to join on is not cluster_id in that file but cl which will should map on to the values you’re observing in cluster_alias. Unfortunately I don’t know myself why those values are so large when compared to the number of clusters.

We have a few python/jupyter notebook tutorials available that show how to merge the cell and cluster data. You can check out this one: 10x RNA-seq clustering analysis and annotation (CCN20230722) — Allen Brain Cell Atlas - Data Access for more information on the cluster dataset and this one: 10x RNA-seq gene expression data (part 1) — Allen Brain Cell Atlas - Data Access which is the first in a set of two that uses the merged cell and cluster data. Look for cell_extended in the previously linked, “part 1” notebook.

Please reach out if you run into more issues.

Good luck!

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Additionally, there is a tutorial to help get you started using the cache object that those two notebooks use here: Getting started — Allen Brain Cell Atlas - Data Access

The full set notebooks that you can run for yourself can be found is this repo here: abc_atlas_access/notebooks at main · AllenInstitute/abc_atlas_access · GitHub

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