Seurat: CreateSeuratObject error, please help
I want to make Seurat Object because I need gene expression matrix. My data form is cell.tsv, feature.tsv and .mtx
This is my code and error.
barcodes <- read.table("4861STDY7387182_cells.tsv", header = TRUE, sep = "\t")[,1]
feature <- read.table("4861STDY7387182_features.tsv",header = FALSE)
matrix <- Matrix::readMM("4861STDY7387182.mtx")
seurat_obj <- CreateSeuratObject(counts = matrix, meta.data = data.frame(Barcode = barcodes), features = feature)
Error: Not enough features for the counts matrices provided
And this is my data structure
> head(barcodes)
[1] "4861STDY7387182_AAACCTGAGCCAGTAG" "4861STDY7387182_AAACCTGAGCGATAGC" "4861STDY7387182_AAACCTGAGGGTGTTG" "4861STDY7387182_AAACCTGCACACTGCG" "4861STDY7387182_AAACCTGCAGGTCCAC" "4861STDY7387182_AAACCTGCATACAGCT"
> head(feature)
V1
1 RP11-34P13.3
2 FAM138A
3 RP11-34P13.7
4 RP11-34P13.8
5 RP11-34P13.9
6 FO538757.2
> str(feature)
'data.frame': 28614 obs. of 1 variable:
$ V1: chr "RP11-34P13.3" "FAM138A" "RP11-34P13.7" "RP11-34P13.8" ...
> str(matrix)
Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
..@ i : int [1:18607530] 22 27 28 33 40 41 49 55 56 72 ...
..@ j : int [1:18607530] 0 0 0 0 0 0 0 0 0 0 ...
..@ Dim : int [1:2] 28614 6356
..@ Dimnames:List of 2
.. ..$ : NULL
.. ..$ : NULL
..@ x : num [1:18607530] 1 1 3 1 5 1 1 1 1 1 ...
..@ factors : list()
I think each data have same row, how can I solve this matter? I tried it for a few days.
1 answer
A quick and dirty way to create a Seurat object from this data will be as follows:-
In a directory do the followings-
awk '{print $1}' 4861STDY7387182_cells.tsv |sed '1d' >barcodes.tsv
cp 4861STDY7387182_features.tsv features.tsv
cp 4861STDY7387182.mtx matrix.mtx
#gzip the files
gzip barcodes.tsv
gzip features.tsv
gzip matrix.mtx
Now in R do the following-
library(Seurat)
data_dir <- "/path_to_above_gzip_files/"
data <- Read10X(data.dir = data_dir, gene.column = 1)
seurat_obj <- CreateSeuratObject(counts = data)
# Add metadata to Seurat object
barcodes <- read.table("4861STDY7387182_cells.tsv", header = TRUE, sep = "\t")
seurat_obj <- AddMetaData(object = seurat_obj, metadata = barcodes)
head(seurat_obj@meta.data)
orig.ident nCount_RNA nFeature_RNA DonorID log2p1_count n_genes percent_mito BiopsyType
4861STDY7387182_AAACCTGAGCCAGTAG 4861STDY7387182 6364 2046 A13 12.63594 2046 0.03048397 Organ_Donor
4861STDY7387182_AAACCTGAGCGATAGC 4861STDY7387182 15358 3644 A13 13.90680 3644 0.04688111 Organ_Donor
4861STDY7387182_AAACCTGAGGGTGTTG 4861STDY7387182 7457 2367 A13 12.86457 2367 0.07241518 Organ_Donor
4861STDY7387182_AAACCTGCACACTGCG 4861STDY7387182 11614 3293 A13 13.50370 3293 0.04640951 Organ_Donor
4861STDY7387182_AAACCTGCAGGTCCAC 4861STDY7387182 14388 4034 A13 13.81268 4034 0.03697526 Organ_Donor
4861STDY7387182_AAACCTGCATACAGCT 4861STDY7387182 5634 1748 A13 12.46020 1748 0.03461129 Organ_Donor
Location Binary.Stage phase broad_celltypes general_celltypes fine_celltypes
4861STDY7387182_AAACCTGAGCCAGTAG endometrium_enriched Proliferative G1 Stromal eS eS
4861STDY7387182_AAACCTGAGCGATAGC endometrium_enriched Proliferative G1 Stromal eS eS
4861STDY7387182_AAACCTGAGGGTGTTG endometrium_enriched Proliferative G1 Immune Lymphoid Lymphoid
4861STDY7387182_AAACCTGCACACTGCG endometrium_enriched Proliferative G1 Stromal eS eS
4861STDY7387182_AAACCTGCAGGTCCAC endometrium_enriched Proliferative G2M Stromal eS eS
4861STDY7387182_AAACCTGCATACAGCT endometrium_enriched Proliferative G1 Stromal eS eS
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