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).

Nov 30, 2020 · ATACseq 一般人种要求 50M 以上比对的 fragments (reads), 因为线粒体 DNA 没有核小体结合，测序出现大量线粒体数据是正常的，线粒体数据占比在 20-80% 都有可能。 ATACseq 分析流程如下图所示。 质控、比对、peak calling 是必须的上游分析，Motif 等下游分析是个性化的。 下载参考基因组、建立索引、移除不需要区域等。 参考基因组在 GENCODE 下载。 一般用 bowtie2 比对，建立 bowtie2 索引。 一般只分析常染色体，并移除 Blacklist 和线粒体 …

ATAC-seq与ChIP-seq calling出来的peak代表的意义是不同的: ChIP-seq 是用目的蛋白的抗体去拉蛋白，进而把目的蛋白结合的DNA片段也拉下来，然后把 DNA 片段映射到基因组，在基因组上的结合位置就会有DNA 片段堆叠，将这些DNA片段堆叠用柱状图画出来，就会得到所谓的Peak ...

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.

Sep 2, 2019 · ATAC-Seq is a method to investigate the chromatin accessibility and the genome is treated with a transposase (enzyme) called Tn5. It marks open chromatin regions by cutting and inserting adapters for sequencing.

One quality metric for peak calling is to calculate the fraction of reads in peak (FRiP) score. For ATAC-seq, the FRiP score is recommended to be >0.2, with >0.3 as optimal.

In this tutorial we use an R / Bioconductor package ChIPseeker, to have a look at the ATAC / ChIP profiles, annotate peaks and visualise annotations. We will also perform functional annotation of peaks using clusterProfiler.

ATAC-Seq (Assay for Transposase-Accessible Chromatin with high-throughput Sequencing) is a method for determining chromatin accessibility across the genome. It utilizes a hyperactive Tn5 transposase to insert sequencing adapters into open chromatin regions (Fig. 1).

ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) is a method for determining chromatin accessibility across the genome. It utilizes a hyperactive Tn5 transposase to insert sequencing adapters into open chromatin regions.

Aug 20, 2024 · We start by creating a Seurat object using the peak/cell matrix and cell metadata generated by cellranger-atac, and store the path to the fragment file on disk in the Seurat object: What if I don’t have an H5 file? The ATAC-seq data is stored using a custom assay, the ChromatinAssay.