From the bench
to the analysis

Bench scientists rarely see how their data are analysed; analysts rarely see where the data come from. This tutorial follows one sample from the bench to the result, with animations and real data, and shows where in the lab each QC metric is born.

Single-cell RNA-seq →Whole-exome sequencing (WES) →

Single-cell RNA-seq

From a piece of tissue to a cell atlas

1Dissociation
2Droplets
3Cell barcodes, UMIs and reverse transcription
4Library prep and sequencing
5Cell Ranger
6Quality control
7Normalization
8Variable genes and PCA
9Clustering
10UMAP
11Marker genes and cell-type annotation
12Beyond

Data: 10x Genomics 3k PBMCs (2,700 cells)

Whole-exome sequencing (WES)

From a tumour and a blood sample to a mutation landscape

1Samples
2Library prep and exome capture
3Sequencing and coverage depth
4Alignment
5Somatic variant calling
6Annotation and the MAF file
7The cohort landscape
8Tumour mutational burden (TMB)
9Mutation spectra and signatures
10Driver genes and hotspots
11Mutations and outcome
12Beyond

Data: TCGA-LAML (shipped with maftools, 193 patients)

Bench

What each step does and which biases it introduces, at the level of principles.

Where metrics come from

Every QC metric traced back to the step that produces it. Glossary →

Analysis

Drag the parameters on real data and watch the result change.

From the benchto the analysis