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10x Genomics
Chromium Single Cell ATAC

Running Multi-Library Samples

Aggregation and Custom Configuration

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:

  1. You created one library, but sequenced it more than once. This might have been to increase coverage depth, or for some other reason. You might have sequenced the library across different lanes of the same flowcell, or across multiple flow cells. In any of these cases, provided that this all comes from a single library, you can analyze these runs as a single sample using cellranger-atac count by Specifying Input FASTQs.
  1. 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.

  2. 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.