Any alternatives to Cellranger aligner that Seurat can read?
Are there good alternatives to Cellranger aligner that Seurat can read? Or any methods of converting default output from Star to the Seurat readable format?
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ATpoint
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louis-gil •
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Seurat just takes a count matrix with cells as columns and features as rownames. There are a ton of programs now for processing single-cell data, so any specific advice would need more information about your project structure.
The output of cellranger is compressed in 3 files (barcodes, features, matrix) which contain a compression of the count matrix and HTO info. Seurat, decompressed into a count matrix. I'm basically asking if there are any programs that use the same output as cellranger.
Seurat has a function (Read10X) to make it easier to read Cell Ranger output. It converts that output to a matrix. You don't have to use that function. CreateSeuratObject() requires a standard R matrix.