Cell-by-Feature Data Tables

Files containing putative cells only:

[sample_name]_RSEC_MolsPerCell_MEX.zip
[sample_name]_DBEC_MolsPerCell_MEX.zip

Unfiltered file containing all cell indexes with >=10 total reads

[sample_name]_RSEC_MolsPerCell_Unfiltered_MEX.zip

The number of molecules of each bioproduct from each cell is represented in the matrix market exchange (MEX) format. The MEX format is an efficient way to store sparse data, and is a common input format for many single-cell analysis tools. The MEX.zip output files contain three separate gzip compressed files that together represent the molecule counts of each bioproduct in each cell. By convention, these files are named:

barcodes.tsv: Containing a list of cell indexes (integer between 1 and 384³), one per row.
features.tsv: Containing a list of bioproducts detected, one per row. For improved compatibility, this file contains three columns, the first two of which are a duplicated gene symbol or AbSeq, and a third which indicates mRNA (Gene Expression) or AbSeq (Antibody Capture) types.
matrix.mtx: Containing a three column per row representation of molecule counts. First column is the 1-based row number from features.tsv (bioproduct). Second column is the 1-based row number from barcodes.tsv (cell). Third column is the molecule count detected for that bioproduct in that cell.

Cell indexes in the barcodes.tsv file are sorted numerically. Bioproducts in the features.tsv file are sorted alphabetically.