Question: What is the difference between the filtered and the raw (unfiltered) feature-barcode matrix?
Answer: The raw gene-barcode matrix includes all valid barcodes from GEMs (Gel Bead-In EMulsions) captured in the data. However, because most GEMs do not actually contain cells, it follows that most barcodes in the data do not correspond to cells, but rather background noise (e.g. GEMs with free-floating mRNA from lysed or dead cells).
The filtered gene-barcode matrix excludes barcodes that correspond to this background noise. This can be visualized in the barcode vs UMI count rank plot in the web summary file. In the example plot below, UMI counts are on the y-axis ranging from 0 to 10,000 in log scale. Barcodes are on the x-axis, ranked from 0 to 1,000,000 also in log scale. Cell-associated barcodes as determined by the cell-calling heuristic are in blue while background barcodes are in gray.
For more information on gene-barcode matrices please see this page. For more information on the cell-calling heuristic, please see the "Calling Cell Barcodes" section of the algorithms overview page.