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I'm trying to analyze visium-hd data using Seurat. In tutorial, there is no filtering step for removing low quality bins. Because there are several low quality bins in my sample, I should filter those bins now.
When I filtered the bins following parameters(nCount_RNA, nFeature_RNA and percent.mt) using 'subset' function, it removed other binning data.
> hd_obj2_sel1 <- subset(hd_obj2,subset = percent.mt_Spatial.008um < 10 & nCount_Spatial.008um > 100 & nFeature_Spatial.008um > 50)
Spatial.002um assay doesn't leave any cells, so it is removed
Spatial.016um assay doesn't leave any cells, so it is removed
Of course, I can try to analyze again using other bins. However, I want to know how to leave other assays. If not, are there any suggestions for filtering low quality bins?
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Hello :)
I'm trying to analyze visium-hd data using Seurat. In tutorial, there is no filtering step for removing low quality bins. Because there are several low quality bins in my sample, I should filter those bins now.
When I filtered the bins following parameters(nCount_RNA, nFeature_RNA and percent.mt) using 'subset' function, it removed other binning data.
Of course, I can try to analyze again using other bins. However, I want to know how to leave other assays. If not, are there any suggestions for filtering low quality bins?
Thank you in advance :)
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