I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples.

Zeeshan Ahmed,Duygu Ucar

doi:10.7717/peerj.4040

Zeeshan Ahmed, Duygu Ucar

Open Access

https://doi.org/10.7717/peerj.4040

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Journal: PeerJ	Publication Date: Nov 22, 2017
Citations: 20	License type: CC BY 4.0

Affiliation: University of Connecticut Health Center, Jackson Laboratory

Abstract

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross-platform, user-friendly and customized desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (FASTQC, Trimmomatic, BWA, Picard, ATAC_BAM_shiftrt_gappedAlign.pl, Bedtools and Macs2) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+T cells and a feature-based comparison is performed with some available interactive LIMS (Galaxy, SMITH, SeqBench, Wasp, NG6, openBIS). I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists. Additionally, I-ATAC is capable of processing WGS and ChIP-seq samples, and can be customized by the user for one-independent or multiple-sequential operations.

Highlights

Assay for Transposase-Accessible Chromatin with high throughput Sequencing (ATACseq) is developed to profile chromatin accessibility from small cell numbers, making it uniquely suited to study epigenomic profiles of human clinical samples with a systemsHow to cite this article Ahmed and Ucar (2017), I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples
The traditional way of generation sequencing (NGS) data pre-processing is based on running a series of command-line applications, which requires good programming skills and the ability to work in the UNIX environment
The focus of this study is to develop an interactive, cross platform software for ATAC-seq data pre-processing

Summary

Introduction

Assay for Transposase-Accessible Chromatin with high throughput Sequencing (ATACseq) is developed to profile chromatin accessibility from small cell numbers, making it uniquely suited to study epigenomic profiles of human clinical samples with a systemsHow to cite this article Ahmed and Ucar (2017), I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples. Assay for Transposase-Accessible Chromatin with high throughput Sequencing (ATACseq) is developed to profile chromatin accessibility from small cell numbers, making it uniquely suited to study epigenomic profiles of human clinical samples with a systems. ATAC-seq generates libraries via a simple twostep protocol using hyperactive Tn5 transposase, which inserts itself to open chromatin sites and generate double-strand breaks. ATAC-seq is attracting a growing interest in genomics applications due to its simple protocol, high sensitivity, and low expectations for starting material amounts (500–50,000 cells) (Tsompana & Buck, 2014). Data processing and management of samples generated by this new assay are becoming an important first step to studying the open chromatin sites in diverse human cells. Several integrated platforms exist to help in managing and building pipelines for NGS data pre-processing e.g., Galaxy (Scholtalbers et al, 2013; Giardine et al, 2005), SMITH (Venco et al, 2014), SeqBench (Dander et al, 2014), Wasp (McLellan et al, 2012), NG6 (Mariette et al, 2012), openBIS (Bauch et al, 2011), etc

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