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!


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.