A standalone software platform for the interactive management and pre-processing of ATAC-seq samples
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Genomics
- Keywords
- ATAC-seq, Genomics, Data, Management, Pipeline, Pre-Processing
- Copyright
- © 2017 Ahmed et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. A standalone software platform for the interactive management and pre-processing of ATAC-seq samples. PeerJ Preprints 5:e2942v1 https://doi.org/10.7287/peerj.preprints.2942v1
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 uncover 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 desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (e.g., FASTQC for quality checking) 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. 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.
Author Comment
This is a submission to PeerJ for review.