atac-seq-feature-matrix-construction

atac-seq-feature-matrix-construction

Summary

Construction and ingestion of scATAC-seq peak accessibility matrices into a unified project object for joint multiome analysis. This skill enables alignment of chromatin accessibility data with paired gene expression matrices to produce integrated reduced-dimension embeddings.

When to use

When you have processed scATAC-seq data (peak calling complete, cell-barcode matrix generated) and need to register it into ArchR for downstream multiome analysis alongside scRNA-seq gene expression data. Specifically, apply this skill when initiating a paired scATAC-seq and scRNA-seq analysis workflow and the peak matrix has not yet been loaded into an ArchR project object.

When NOT to use

• Input is already an ArchR project object with feature matrix loaded — use addGeneExpressionMatrix directly instead
• Peak matrix has not been quality-filtered or called — first perform peak calling and barcode filtering upstream
• Cell barcodes between scATAC-seq and scRNA-seq samples do not align or originate from different cell populations — resolve barcode mapping before import

Inputs

• scATAC-seq peak-by-cell matrix (sparse or dense format)
• Cell metadata (barcodes, sample IDs, cluster assignments)
• ArchR project object (new or existing)

Outputs

• ArchR project object with registered peak accessibility matrix
• Internal feature matrix representation aligned to cell barcodes
• Project metadata structure ready for multiome integration

How to apply

Load your scATAC-seq peak matrix (rows = peaks, columns = cells with barcodes) and associated metadata (cell clusters, sample annotations) into R. Call importFeatureMatrix to register the feature matrix into a new or existing ArchR project object, which creates a standardized internal representation. The function ingests the peak-by-cell matrix and aligns cell identifiers across modalities. Verify that cells are successfully registered by checking project dimensionality and cell count. Once importFeatureMatrix completes, proceed to addGeneExpressionMatrix to append the scRNA-seq gene expression matrix to the same project, ensuring barcode alignment between modalities.