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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Could you please tell me how to use ReadXenium() to load the New 10x Xenium Bundle?_no more "cell_feature_matrix" #9468

Closed imamura-masaki closed 3 days ago

imamura-masaki commented 1 week ago

A new Xenium Bundle using 5k panels has been released by 10X (https://www.10xgenomics.com/datasets/preview-data-xenium-prime-gene-expression), but I cannot load it using ReadXenium(). There was a similar question before, and when I entered the same code, the following error occurred. It seems that the cause is that barcode.tsv.gz does not exist in the cell_feature_matrix file. Could you please tell me how to solve this problem and the code?

data <- ReadXenium(data.dir = DIR) Read10X(data.dir = file.path(data.dir, "cell_feature_matrix.zarr")) でエラー: Barcode file missing. Expecting barcodes.tsv.gz Called from: Read10X(data.dir = file.path(data.dir, "cell_feature_matrix.zarr"))

longmanz commented 3 days ago

Hi, Thank you for reporting this. Our team has implemented a new loading function for the new 10x bundle. You can try it our with our develop version:

# Enter commands in R (or R studio, if installed)
# Install the remotes package
install.packages('remotes')
remotes::install_github(repo = 'satijalab/seurat', ref = 'develop')
library(Seurat)

Feel free to reopen it if the issue persists.