Interpreting Single Cell Gene Expression Data With and Without Intronic Reads

Technical Note, Last Modified on June 21, 2022, Permalink

CG000554_Interpreting_SingleCellGEX_with_introns_RevA.pdf

In whole transcriptome single cell data from Chromium Single Cell 3’ and 5’ products, reads primarily map to exonic regions derived from mature spliced mRNA transcripts. However, reads may also map entirely or partially to intronic regions (Figure 1). This Technical Note evaluates the effects of counting intronic reads for Single Cell Gene Expression cellular data.