cellranger count I got two relevant for further analysis folders:
raw_gene_bc_matrices. What is the difference between them? What does
cellranger filter out, and what should we preferably use for further analysis?
I'm unsure whether this is the answer you are looking for, but when looking into 10X cellranger documentation for the Matrices Output:
Unfiltered gene-barcode matrices: Contains every barcode from fixed list of known-good barcode sequences. This includes background and non-cellular barcodes.
Filtered gene-barcode matrices: Contains only detected cellular barcodes.