cellranger-arc-multiome

Process 10x Multiome ATAC+GEX data by running the cellranger-arc pipeline to demultiplex single-index ATAC libraries and align paired modalities from the same cells. It executes end-to-end steps including mkfastq, count, aggregation, and reanalysis.

Configure a libraries CSV for 10x Multiome ARC processing by including combined ATAC and GEX library entries. The pipeline enforces specific rules to ensure both modalities are present before running cellranger-arc count on your FASTQ data.

Yes, you can demultiplex single-index ATAC libraries within a combined multiome workflow. The pipeline handles single-index ATAC demultiplexing directly alongside GEX alignment to process paired data from the same cells.

The cellranger-arc pipeline generates joint matrices and depth-fragment data outputs. These filtered matrices and fragment files are produced ready for downstream analyses using tools like Seurat, Signac, and ArchR.

Yes, the 10x Multiome ARC pipeline supports aggregated results and reanalysis steps. It provides a complete end-to-end workflow that includes mkfastq, count, aggregated result generation, and reanalysis for paired ATAC and GEX data.

The best way to handle paired ATAC and gene expression data is using a combined libraries CSV to configure the multiome workflow. This ensures both modalities are processed together through mkfastq and count to generate joint outputs.