What Read Length Do I Choose?

Longer reads can be helpful when dealing with larger genomes, shorter reads may be sufficient for mapping of reads to a small genome and for counting and RNA-Seq profiling experiments.

The Instrument provides flexibility in choosing the number of base pairs (cycles) you can sequence within a single read. The number of cycles chosen defines the output read length. Longer reads provide more accurate information in terms of relative position within the target genome and can be helpful when dealing with larger, more complex genomes. Shorter reads may be sufficient for simple mapping of reads to a small, lower complexity genome and for certain types of experiments (for example, RNA-Seq profiling or counting applications).

Shown below are examples of common applications that can be run on the Instrument. This table is only an example and is not an exhaustive list of all applications that are supported. Refer to https://singulargenomics.com/g4/reagents/ to see what flow cell is best for your application, and how they fit into a run configuration.

Application

Typical Run

RNA Gene Expression

2 × 50 bp, 10 M reads

Single Cell RNA-Seq

130 cycles, 7 500 cells/sample and 20 000 reads/cell

Total RNA-Seq

2 × 100 bp, 50 M reads

Exome

2 × 100 bp, 35 Mb at 100× coverage

Target Enrichment

2 × 150 bp, 800 Kb at 4000× coverage

For more information, see the G4 Best Practices and Quality Control Guide, reach out to your Field Application Scientist, or contact Customer Care.

October 2023