Question: Should I include introns for Targeted Gene Expression data analysis?
Answer: Although we recommend including introns for whole transcriptome gene expression data analysis, the recommended (and default) mode for Targeted Gene Expression analysis is exon-only. This is because 10x Genomics supported baits are designed to capture exons only.
Note: The Targeted Gene Expression assay has been discontinued. For alternative options, please see: What options are there for performing a targeted enrichment for my gene expression libraries?
Related article: Is the Targeted Gene Expression assay compatible with nuclei?