Our bridge procedure successfully mapped the scATAC-seq dataset on our Azimuth reference, enabling joint visualization of scATAC-seq and scRNA-seq data (Fig. 2c), as well as automated annotation of scATAC-seq profiles with accompanying prediction scores. Reference-mapping also aligned shared cell populations across multiple samples, mitigating sample-specific batch effects. Query samples representing CD34+ BMMC fractions mapped exclusively to the HSC and progenitor components in the reference dataset, demonstrating that bridge integration can robustly handle cases where the query dataset represent a subset of the reference, while whole fractions mapped to all 35 cell states (Supplementary Fig. 1a).
