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Alternatively, Cell Ranger reference can be added beforehand, to the Library file management page (on the Other library files tab). At the moment, the following references are available for download from Partek: hg38, mm10, and hg38-mm10 (chimaeric genome).

The sample table under Input options has one row per sample. Image file is required, and that is a single hematoxylin and eosin brightfield image in either .jpg or .tiff format. Click on the Browse button under Browse image file and the file browser will come up. Point to the image file and push Continue. Probe set file is optional; it is a .csv file specifying the probe set used (=target panel).

If you want to specify sample's slide and area information, tick mark the box by the Use slide serial number file and then click Browse to point to the file. The file should be tab-delimited with samples on rows. The first column is the sample name, slide name is on the second column, slide area on the third column.

Click on the Configure link in the Advanced options section to open the Advanced options dialog (Figure 5). Use R1 length to hard trim the R1 reads to specified length; use R2 length to hard trim the R2 reads to specified length. Use the Memory limt option to cap the RAM usage (in GB).