Question: Can I analyze only the ATAC data from my single cell multiome experiment?
Answer: Yes, it is possible to analyze just the individual ATAC library from a multiome assay using cellranger-atac count. It requires a minimum of v2 of Cell Ranger ATAC to be installed on your system.
For the software to correctly recognize and process the data, it is necessary to specify the type of chemistry. This is in order to distinguish between an ATAC library of a multiome assay vs standalone single assay ATAC library. The cellranger-atac count analysis needs to include --chemistry=ARC-v1 flag to indicate that it is a library from the multiome assay.
Alternatively, if you have already run cellranger-arc count to analyze your multiome experiment, and find the GEX library to be low quality, you can look at an ATAC-only web summary. The standalone ATAC web summary can be found in the intermediate folder at SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/files/web_summary.html
Related article: Can I analyze only the Gene Expression data from my single cell multiome experiment?
Note: This type of analysis is not officially supported. We do not recommend or advise the analysis of single modalities from the multiome assay. The main benefits of the multiome assay i.e. joint cell-calling and feature linkages will not be available when analysis is carried out in this way.