Question: Which reads are considered for UMI counting in
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)
- A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise.