Export MEX Expression Matrix
For export in MEX format, a number of options can be specified (figure 3.4):
Figure 3.4: Options for export of expression matrix in Mex format.
- Cell format. Can be specified to include both the sample and barcode. Hover the mouse over this setting to see the possible options. Often the barcode in itself is sufficient as a unique identifier of cells. However, when an expression matrix contains multiple samples, the cell format must also include the sample, otherwise the export will fail.
- Export normalized. If selected and the matrix has been normalized with Normalize Single Cell Data (see Normalize Single Cell Data), the normalized expressions will be exported instead of the raw counts. If the matrix has not been normalized, the export will fail.
- Use compression. Select among gzip, zip or no compression which is default.
- Output file name. Shows the name of the file. This can be customized by changing the default pattern in Custom file name.. The default configuration will export to a sub-directory named after the expression matrix ({name}).
The export outputs barcodes, features, and expressions to barcodes.tsv, features.tsv, and matrix.mtx, respectively.
If the matrix is an Expression Matrix with spliced and unspliced counts (
), two additional files are produced containing spliced (spliced.mtx) and unspliced (unspliced.mtx) counts.