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As part of a data analysis project, I encountered two kinds of single-cell assays for transposase-accessible chromatin using sequencing (single-cell ATAC seq) methods. The first uses combinatorial indexing (also called sci-ATAC seq [link]), whereas the other counts the number of Tn5 cuts in peaks (called sc-ATAC seq [link]). I'm not a trained cell biologist or biotechnologist so I am possibly overlooking subtle similarities between the two methods here.

To my knowledge, sci-ATAC seq generates a binarised array, whereas sc-ATAC seq generates a counts matrix. (I'm also aware that there are post-processing tricks to convert binarised arrays to other array types, eg, normalised counts arrays.)

My question is, what about combinatorial indexing results in the array being binary rather than integer-valued? I'm looking for an explanation that relates the data collection method and combinatorial indexing with the resulting array type.

Thanks in advance!

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