Hello, this is my first post on biostars! Thank you in advance for any help.
I'm having trouble converting a RNA-seq gene count sparse matrix from .txt to MatrixMarket .mtx file. I'm working with the gene count sparse matrix from this dataset.
And wanted to load the matrix in R so that I can filter cells by barcode out of the dataset. The first line of the .txt file is:
%%MatrixMarket matrix coordinate integer general
So I figured I'd be able to use the readMM() function however doing this gave me the error message:
Error in readMM(file = "~/scratch/rtrujillo/RNA-seq/sci-seq/gene_count.txt") : file is not a MatrixMarket file
How can I load this file in R?
2 answers
It works on my machine:
#/ download
wget -O - https://shendure-web.gs.washington.edu/content/members/cao1025/public/mouse_embryo_atlas/gene_count.txt | head > data.txt
#/ read in R:
library(Matrix)
Matrix::readMM("data.txt")
26183 x 2058652 sparse Matrix of class "dgTMatrix"
(...)
Weird, I removed gene_count.txt and ran the script successfully after redownloading it with wget. I had used curl before:
and never did anything after to manipulate the file. Is it possible the curl command altered gene_count.txt in some way wget didn't?
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