Question: What factors contribute to a low transcriptome mapping rate in Cell Ranger?
Answer: There are many factors that contribute to low read mapping rate.
Factors related to the Cell Ranger reference package:
- Completeness of the assembly used for reference: more complete genomes are better.
- The complexity of the genome/repeats: the repetitive nature of the genome can negatively influence mapping. Reads aligning non-uniquely to multiple genes are not considered for UMI counting.
- The number of overlapping gene annotations: reads aligning uniquely but to overlapping gene annotations are not considered for UMI counting.
Factors related to library prep or sequencing quality:
- RNA/sample quality: contamination of the sample with cells/RNA from other species would impact mapping rates.
- Read quality: higher quality reads should improve mapping rate.
- Read length: longer reads improve mapping, but only moderately.
If you encounter any other factors that you believe are influencing your mapping rate, please email [email protected].