Replies: 2 comments 2 replies
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the actual question is what files are in your /outs folder localdir <- "/brahms/lis/visium_hd/Visium_HD_Public_Data/HD_public_data/Visium_HD_Mouse_Small_Intestine/outs" |
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what should be the input file? Would specifying file name work for loading the data: Load10X_Spatial(data.dir = localdir, filename="filtered_feature_bc_matrix.h5") ? |
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You don't need to mention the file name in case you use the bin.size option. It will read the necessary files. |
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Figured it out. thank you |
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For the visium HD tutorial (https://satijalab.org/seurat/articles/visiumhd_commands_intro) I will likely have to upgrade to Seurat v5 correct?
I have downloaded the 8 and 16 um bins from 10x and created path to file with the directory containing the spatial folder, filtered features.h5 file, and others; however, in contrast to visium v2 the Load10x_Spatial command here includes bin.size and my question is where is this data stored in the directory?
object <- Load10X_Spatial (data.dir = localdir, bin.size = c(8, 16))
Thank you!
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