Space Ranger1.3 (latest), printed on 07/03/2022
The spaceranger count pipeline accepts slide serial and capture area arguments, in order to use the most precise fiducial and spot coordinates for an experiment.
There are three different ways to specify the slide information in spaceranger count run:
|Space Ranger Arguments||Access to Slide Layout||Internet Access||Details|
||Yes||Yes||The pipeline will download the layout file associated with the supplied serial number.|
||Yes||No||User downloads a layout file for a Visium slide before running the pipeline. Download here|
||No||Optional||The pipeline uses a default layout file for spot and fiducial coordinates. The typical per-spot difference between the default layout and a specific slide is under 10 microns.|