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Asst Prof Dr Zeeshan AHMED edited this page Dec 21, 2017 · 16 revisions

Welcome to the I-ATAC wiki!

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.

Workflow

ATAC-seq data pre-processing workflow, file types and integrated tools.

Main Interface Graphical User Interface of Processing module of I-ATAC: Create and run data processing jobs.

Data Input Data processing step 1

Data Processing Data processing step 2

Settgins Graphical User Interface of Settings module of I-ATAC: Set parameters and user credentials.

Publication: Ahmed Z, Ucar D. (2017) I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples. PeerJ 5:e4040

I-ATAC Team:

  • Asst. Prof. Dr. Zeeshan Ahmed
  • Asst. Prof. Dr. Duygu Ucar (The Jackson Laboratory, USA)

Project Page: I-ATAC

Disclaimer of Warranties and Liabilities The Jackson Laboratory provides the software "as is" without warranty of any kind, implied or expressed. You assume full responsibility and risk of loss resulting from your downloading and use of the content of the software. We expressly disclaim any warranty of merchantability, title, security, accuracy and non-infringement. In no event shall The Jackson Laboratory be liable for any claim, damages or other liability arising from the software or the use of the software. You may only use our content in academic research but not for commercial purposes. The software is provided as an information resource only, and should not be used or relied on for any diagnostic or treatment purposes.

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