MSE Research Project Database

Improving peak calling for ATAC sequencing data


Project Leader: Jan Schroeder
Primary Contact: Jan Schroeder (jan.schroeder@unimelb.edu.au)
Keywords: bioinformatics
Disciplines: Computing and Information Systems
Domains: Convergence of engineering and IT with the life sciences

ATAC sequencing (Assay for Transposase-Accessible Chromatin with high throughput sequencing) is a technology to analyse the accessability of DNA within cells. Being able to measure this property allows the researcher to argue about regulation of genes and their expression, among other things, within a particular cell type of interest.

Current analyes of this data use peak calling methods developed for other technologies (such as ChIP-seq) to infer enrichment of sequencing reads, and therefore open chromatin. While the two tasks are similar, ATAC data has its own particularities. For example, transcription factors bound to the DNA during the experiment can lead to a depletion of signal right in the centre of the peak. This is one of the most useful results from an ATAC experiment, as it not only informs about accessible, but also actively regulated bits of the DNA. Standard peak calling methods are not sensitive to such subtleties in the data, and a dedicated peak calling mehtod for ATAC sequencing is therefore warranted. 

Further information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959825/