Question: Which reads are considered for UMI counting in cellranger count?
Answer: When counting UMIs, Cell Ranger only consider reads that have a valid UMI and a valid 10x barcode. Further, Cell Ranger considers reads which meet all of the following criteria:
- Has a MAPQ of 255
- Maps to exactly one gene (as shown in the GX tag of the BAM file alignment record)
- Overlaps an exon by at least 50% in a way consistent with annotated splice junctions and strand annotation.
Multiple reads that map to the same UMI will only count once. For more information please see Algorithms Overview.