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.
- Short/degraded cDNA: if the cDNA is short/degraded, it can lead to more of TSO carried over into the final library and can lead to low mapping to transcriptome.
If you encounter any other factors that you believe are influencing your mapping rate, please email email@example.com.