ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.

BMC Genomics
Jianhong OuLihua Julie Zhu

Abstract

ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets. We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. W...Continue Reading

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Datasets Mentioned

BETA
SRR891272
SRR891274
SRR891270
SRR5720369
SRR580802
SRR3295017

Methods Mentioned

BETA
ATAC-Seq
ChIP-seq
PCR

Software Mentioned

NucleoATAC
Bowtie2
bamQC
Bioconductor
SRA
seq
GenomicRanges
ggplot2
MACS2
motifStack

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