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?
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.