Question: Can I sequence longer than 91-98bp on Read 2 for Single Cell 3' and 5' gene expression libraries?
Answer: For the purpose of gene counting, 98 bases (3' v2 chemistry, 5') or 91 bases (3' v3 chemistry) are sufficient to align confidentially to the transcriptome. For longer sequence reads, the lower base quality towards the end of the read may impair accurate mapping. Cell Ranger only includes confidently mapped reads and will filter out those that don't map accurately. In addition, having a longer read on the transcript may increase your chance of having it mapped to multiple genes - which will also be filtered out. Conversely, shorter reads have increased chances of multi-mapping. For this reason, we recommend following the recommended read length.
Products: Single Cell Gene Expression, Single Cell Immune Profiling