Question: Can I decrease the sequencing length of Read 2 for Single Cell Gene Expression assays?
Answer: For Read 2 in the Gene Expression component of our Single Cell 3' or 5' assays, the recommendation of 90-91 cycles is a balance between obtaining enough sequence for high mapping rates while also avoiding sequencing into the poly(A) tail. A lower number of cycles can negatively affect the mapping rate of reads to the reference transcriptome.
Below is a figure demonstrating how the fraction of reads mapped confidently to the transcriptome decreases with shorter Read 2 lengths. When using read trimming, which was implemented in Cell Ranger 4.0, mapping rates decline noticeably if Read 2 is shorter than ~65bp. If read trimming is not performed, mapping rates decline if Read 2 is shorter than ~90bp.
Products: Single Cell Gene Expression, Single Cell Immune Profiling