10x Genomics

Recommendation on Including Introns for Gene Expression Analysis

Updated: May 17, 2022

In 10x Genomics whole transcriptome Gene Expression data, intronic mapped reads account for 20-40% of the reads. These reads have traditionally not been counted by default in Cell Ranger. Recent data has indicated that intronic reads are usable data (they arise from poly-A tracts in the transcripts, and are not generated via priming from genomic DNA). Including intronic reads, for both cellular and nuclei samples, could lead to higher sensitivity (higher UMI counts, more genes per cell) and less wasted sequencing.

To empower our customers with higher sensitivity, Cell Ranger v7.0 includes intronic reads by default towards UMI counting. Intronic reads can be included manually in your analysis with Cell Ranger v5.0 - 6.1 with the following options:

Frequently asked questions:

Example datasets:

If you have any concerns or questions, please reach out to the 10x Genomics support team at [email protected]