# Raw vs Filtered in the output of cellranger count

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?

• Mostly people use the filtered gene bc matrix. Take a look at the guided tutorial for the r package Seurat if you're new to 10x and /or single cell (satijalab.org/seurat/pbmc3k_tutorial.html) May 26, 2018 at 12:21