Question: Why did transcriptome mapping rates increase in Cell Ranger 1.3 compared to previous versions?
Answer: Prior to Cell Ranger version 1.3, if a read mapped to multiple loci from the same gene, it was considered ambiguous and didn't count towards the transcriptome mapping rate.
Starting in Cell Ranger 1.3, a read that maps to multiple loci in the genome is considered mapped to the transcriptome if either:
- The candidate loci are all in the same gene.
- Only one candidate locus is exonic and the rest are non-exonic.
Note that the STAR alignment parameters did not change.