Question: When does Cell Ranger DNA trigger alerts?
Answer: Alerts are triggered based on a variety of metrics. The complete list can be found with the Cell Ranger DNA software distribution, in the the file
For some alerts, there are two levels of severity: WARN and ERROR. A warning is an indication that the metric falls outside the expected range. An error is more extreme and usually indicates an issue that needs to be addressed.
For example, the "not_enough_cells" alert triggers a warning when the number of cells detected is below 250. A typical experiment might target 1000 cells, and only 250 detected could indicate a lack of capture efficiency or some other aspect of the sample that is suboptimal. However, it is not a complete failure in that the data from those 250 cells is likely usable. On the other hand, an error is triggered if the number of detected cells is less than 10, since that likely indicates outright failure of the experiment.
Any alerts that are triggered are presented in the Web Summary as well as the
alarms_summary.txt file present in the
outs directory that the pipeline generates.