I'm trying to understand how the latest version of cell ranger takes intronic reads into account when performing UMI counting.
They have documented about how UMI counting works but it's only for Cell ranger 3 (https://www.10xgenomics.com/resources/analysis-guides/tutorial-navigating-10x-barcoded-bam-files):
For a UMI to be counted it must meet specific criteria:
- Have a MAPQ score of 255 (see the STAR manual, section 4.2).
- Maps to exactly one gene (as shown in the GX tag of the BAM file)
- Overlaps an exon by at least 50% in a way consistent with annotated splice junctions and strand annotation.
- Records that align to exons will have an RE:A:E tag.
- Remove any records with matching UMI and Barcode values that map to different genes.
Then what is condition for intronic reads to be counted?
Thanks for your help.