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After running cellranger count I got two relevant for further analysis folders: filtered_gene_bc_matrices and raw_gene_bc_matrices. What is the difference between them? What does cellranger filter out, and what should we preferably use for further analysis?

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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.

Source

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