Seurat: CreateSeuratObject error, please help

Question

[mnx0723]

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.

Answer 1

[bk11]

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([e-mail])
                                      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

[mnx0723]

Oh, Thank you!! It helps me