Use read simulators to validate spike in protocol

Status: selected

Praktikum (Bachelor/Master)

Field: Genomics, Simulations

Advisors:  Dr. Julia Engelmann

Courses Required: Practical Bioinformatics I, Transcriptomics with RNA-seq or Sequenzing

Objective: Most algorithms for detection of differentially expressed genes assume that the majority of genes do not change their gene expression level over different conditions. This assumption is used throughout the complete RNA-seq workflow, starting from taking a fixed amount of RNA for sequencing. Recently it has been shown that certain conditions, e.g. constant activation of a transcription factor, can globally affect gene expression. To be able to detect these global changes, new experimental and computational approaches need to be developed. We propose to use foreign organism cells as spike-ins to calibrate for all sources of technical variation and monitor global gene expression shifts.

Data: The FluxSimulator will be used to generate simulated sequencing data.

First-Steps:  get familiar with using the Flux Simulator, make a table of the experimental settings to be analysed.

Questions:  What percentage of foreign organism cells is needed for robust calibration? How does this correlate with sequencing depth? Is the approach robust against varying sequencing depth of different samples? Can we derive a rule-of-thumb about the phylogenetic distance that needs to lie between the organism of interest and the foreign organism?

Start Reading:

FluxSimulator: sammeth.net/confluence/display/SIM/Home and publication

"Revisiting global gene expression analysis" (2012) Loven et al. www.ncbi.nlm.nih.gov/pmc/articles/PMC3505597/