Entering edit mode
15 months ago
biocellbio
•
0
Hi everyone,
I would like to download some 10X Visium spatial transcriptomics data from this publication using this GEO link. It seems they have barcodes, features, and matrix files associated with the spatial data, however, I was under the impression that 10x spatial output is an H5 file.
I am able to download the the barcode, features, and matrix files and load them into a Seurat object using the Read10X command, but can't seem to get anywhere from there in terms of tissue slice or spot coordinates. I was wondering if there is something I am missing in terms of convention for downloading the spatial data. Any help would be greatly appreciated!
At first glance it does not appear that the images or any other data is provided. Looking at
Data accesstab for one of the samples only sequence files appear to be included: https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR13565263&display=data-accessIf there is an associated publication see if it gives any clue as to where other data can be found. It may be up on Zenodo etc.