Cell Ranger ATAC 1.0 (latest), printed on 03/22/2019
As mentioned in the workflow overview, Cell Ranger ATAC, here are three circumstances where combining data from libraries may be needed, from most to least common:
|Neither of the scenarios mentioned below are supported in cellranger-atac 1.0.1. They may be supported in future releases of the software|
You created multiple libraries from multiple samples. This would be the case in many experiments, such as comparing diseased and healthy patients. You can certainly run cellranger-atac count on each library separately, but the version 1.0.1 of the pipeline does not support aggregating analyses across libraries from multiple samples.
You created multiple libraries from the same sample. In this case, most customers can choose to simply treat them as if they were different samples. However, if it is necessary, one may want to pool these libraries and analyze them as a single sample. However, the version 1.0.1 of the pipeline does not support aggregating analyses across multiple libraries from the same sample.