Hello everyone,
I am working on single-cell analysis of my data. From 10X Genomics, I have scATAC-seq data and also multiome (measurements of scRNA + scATAC from the same cell). After using Cell Ranger ARC and analyzing the multiome data, I have wanted to aggregate the multiome ATAC with the individual ATAC samples that I have had following this approach on cell ranger's website.
This step worked wonderfully. However, the multiome barcodes for the merged ATAC (aggregated) do not match the barcodes from the multiome ARC analysis. Because of how the barcodes are getting translated with Cell Ranger ARC. Basically, with multiome assay, there is 1:1 mapping between RNA and ATAC barcodes. However, no such mapping exists if you try to combine scATAC and multiome ATAC data together hence the difference. Now, if possible I would like these aggregated barcodes to match because I have a quality-controlled multiome object with RNA and ATAC information that I am planning to use for my analysis.
Have anyone tried this, and if so how can I match the RNA and ATAC barcodes from the multiome data after aggregation?
Thank you !
