Identifying Correlated Genes for Defining Cluster Identity in scATAC-seq Data.

[annrosebright]

Hello,

I wanted to thank you for creating such a useful tool. I am currently using addGeneIntegrationMatrix to define clusters for my scATAC-seq data, and it's been working great. Even cell types that are transcriptomically similar across stages are getting integrated well with scATAC-seq groups.

I am interested in whether it's possible to extract information about which genes match across RNA-ATAC clusters. Specifically, I would like to know if we can determine whether certain genes in Cluster A RNA have correlating gene scores with Cluster D ATAC. There fore the Cluster D ATAC cells got labeled as Cluster A. I understand that these are most probably variable genes but can we especially identify which among them were matching? This would help us to actually explore some of the information we are interested in RNA.

Thank you for your help.

Best,
Ann