it is said that the features.tsv from Cell Ranger v3 is analogous to the genes.tsv from Cell Ranger v2. So can I change the file name to genes.tsv for Seurat to read it? I know that Seurat has the update version 3 that can read the features.tsv, and I would like to use the old version. So if I change the file name, did it cause any problem?enter image description here

  • $\begingroup$ You can find an answer here: github.com/satijalab/seurat/issues/1196. In brief: Read10X is convenience, you can use the files yourself to generate the matrix but if you only have RNA in your experiment your strategy should work. Did you unzip the file and rename? or rename the zipped file? $\endgroup$
    – Mack123456
    Aug 15 '19 at 21:05
  • $\begingroup$ Thank you for your reply, and I unzip the file and rename it. Much appreciated! $\endgroup$
    – hua
    Aug 15 '19 at 21:47

You can follow the 10X instructions to load your matrix into R: the following is a direct quote from their webpage:

matrix_dir = "/opt/sample345/outs/filtered_feature_bc_matrix/"
barcode.path <- paste0(matrix_dir, "barcodes.tsv.gz")
features.path <- paste0(matrix_dir, "features.tsv.gz")
matrix.path <- paste0(matrix_dir, "matrix.mtx.gz")
mat <- readMM(file = matrix.path)
feature.names = read.delim(features.path, 
                           header = FALSE,
                           stringsAsFactors = FALSE)
barcode.names = read.delim(barcode.path, 
                           header = FALSE,
                           stringsAsFactors = FALSE)
colnames(mat) = barcode.names$V1
rownames(mat) = feature.names$V1

You can then create a seurat object using mat

object <- CreateSeuratObject(mat, project="")

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