What are the major steps in ATAC-seq analysis?

What are the major steps in ATAC-seq analysis?

Here, we discuss the major steps in ATAC-seq data analysis, including pre-analysis (quality check and alignment), core analysis (peak calling), and advanced analysis (peak differential analysis and annotation, motif enrichment, footprinting, and nucleosome position analysis).

How is ATAC-seq used to calculate differential accessibility?

Using an in vivo ATAC-seq data set generated in our recent report, we observed differences in chromatin accessibility patterns depending on the data normalization method used to calculate differential accessibility. This observation was further verified on published ATAC-seq data from yeast.

How is the encode pipeline used in ATAC-seq?

The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment. Pipeline schematic for replicated data View the current instances of the pipeline for replicated data Pipeline schematic for unreplicated data

Which is the default peak caller for ATAC seq?

Currently, MACS2 is the default peak caller of the ENCODE ATAC-seq pipeline. To the best of our knowledge, only one peak caller is specifically developed for ATAC-seq [ 61 ]. All others are adopted from ChIP-seq and DNase-seq with the assumption that ATAC-seq peak patterns share the same properties.

How is ATAC seq used to map open chromatin?

To map the open chromatin landscape in relation to T2D, we performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) in human pancreatic islets from T2D and non-diabetic donors. ATAC-seq is a sensitive recently developed method with ability to map open chromatin in a small number of cells 16.

How is TF binding motif analysis of ATAC-seq performed?

TF binding motif analysis of ATAC-seq data was performed using HOMER v4.7.2 17. Only known motifs from HOMER’s motif database were considered. We studied motifs enriched in ATAC-seq peaks of non-diabetic donors, and motifs enriched in T2D peaks relative non-diabetics.