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?
You can follow the 10X instructions to load your matrix into R: the following is a direct quote from their webpage:
library(Matrix) 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="")