Topic
Sequencing depth and saturation
Do I need more reads, or more replicates?
Depth past saturation buys nothing; replicates almost always buy more than depth. Saturation curves, Cell Ranger sequencing saturation, and the number of detected genes versus reads tell you which side of the curve you are on.
- How to Tell If You Sequenced Deep Enough in ATAC-seq
Before you pay for another lane, find out whether your ATAC-seq libraries are out of depth or out of complexity, and whether a third replicate would help more.
- How to Tell If You Sequenced Deep Enough in Variant Calling
Mean coverage looks fine, the VCF looks clean, and you still cannot say whether the missing variants are absent or just unsampled.