Most of the deep sequencing done in the UWBC DNA Sequencing Facility will be done on “10B” flow cells for the NovaSeq X+ instrument. These flow cells comprise eight lanes, each providing an estimated 1.25B reads, and the reagent kits for the flow cells come in 2×50 bp, 2×100 bp, and 2×150 bp options at increasing cost.
For most single cell RNA-seq projects, the read depth provided by a small number of these individual lanes is sufficient. Sequencing your libraries with less than a full flow cell will almost always be done using the more expensive 2×150 bp reagents, because that read length is needed for the majority of other projects that will fill the remaining lanes on the flow cell. However, 10X Genomics libraries can be sequenced to the required specifications using the cheaper 2×50 bp reagent kits; if your project is large or complicated enough to require more than five lanes of an individual 2×150 bp flow cell, you can save money (and often get more reads) by instead going with your own full 2×50 flow cell instead of buying six or more lanes of a shared 2×150 bp flow cell. For very large projects, we may instead recommend the newer “25B” flow cell, which provides around 25 billion reads at a cheaper price than the equivalent number of reads from 10B flow cells. The 25B is currently only available with 2×150 bp read length kits. In any case, your reads will be trimmed to the appropriate length for 10X Genomics libraries as part of the DNA Sequencing Facility’s data release process.
See: Illumina sequencing prices at the UWBC DNA Sequencing Facility