Format
10x MTX (Matrix Market)
Cell Ranger's three-file sparse output: the coordinate-format matrix plus features and barcodes. Genes are rows, cells are columns.
Extensions: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz · Coordinates: n/a · Specification
From 10x MTX (Matrix Market)
- How to Convert 10x MTX to CSV/TSV count table (Without Losing Your Metadata)
Densifying a sparse 10x matrix for a spreadsheet is usually the wrong call, here's how to do it safely on the rare occasion you can't avoid it.
- How to Convert 10x MTX to h5ad (and Why IDs Go Missing)
The default read call quietly swaps your Ensembl IDs for gene symbols, and the duplicate-name patch that follows hides the damage instead of fixing it.
- How to Convert 10x MTX to Seurat object (and Why IDs Go Missing)
Read10X reads a directory, not a file, and the column you pick for gene names quietly decides how many genes you actually have.
To 10x MTX (Matrix Market)
- How to Convert Seurat object to 10x MTX (Commands, Checks, and Pitfalls)
Pick the wrong Seurat layer, or reach for Matrix::writeMM instead of write10xCounts, and your MTX directory looks complete right up until Scanpy or Cell Ranger tries to load it.