- Peak calling is a computational method used to identify areas in a genome that have been enriched with aligned reads as a consequence of performing a ChIP-sequencing or MeDIP-seq experiment. These areas are those where a protein interacts with DNA.en.wikipedia.org/wiki/Peak_calling
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From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Feb 3, 2020 · 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 …
Comprehensive comparative analysis of 5′-end RNA-sequencing …
Jun 4, 2018 · A direct comparison of 5′-end RNA-seq methods reveals strong performance by CAGE, and identifies differential transcriptional start site usage among brain-related samples.
Comparison of differential accessibility analysis strategies for ATAC ...
Jun 23, 2020 · ATAC-seq peak density and RNA-seq expression density were plotted in R using ggplot2. Fractions of peaks and genes with expression between 1-5 CPM, 5-10 CPM, and >10 …
Productive visualization of high-throughput sequencing data
Oct 1, 2021 · Current high-throughput sequencing techniques (e.g. ChIP-seq, ATAC-seq, and RNA-seq) can use a single run to identify the repertoire of functional characteristics of the …
Peak calling - Wikipedia
Peak calling is a computational method used to identify areas in a genome that have been enriched with aligned reads as a consequence of performing a ChIP-sequencing or MeDIP-seq experiment. These areas are those where a protein interacts with DNA. When the protein is a transcription factor, the enriched area is its transcription factor binding site (TFBS). Popular software programs include MACS. Wilbanks and colleagues is a survey of the ChIP-seq peak c…
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Covering all your bases: incorporating intron signal from RNA-seq …
RNA-seq can be used to characterize and study many RNA types, including non-coding RNAs that regulate a diverse range of cellular processes ... where at its peak it is expressed similarly …
Peak Calling - an overview | ScienceDirect Topics
Methods based on peak calling. The peak callingstrategy is widely used by most methods for pA identification from scRNA-seq data, including scAPA [101], polyApipe …
Calling peaks • Signac - Stuart Lab
Aug 20, 2024 · In this tutorial, we demonstrate how to call peaks on a single-cell ATAC-seq dataset using MACS2. To use the peak calling functionality in Signac you will first need to install MACS2. This can be done using pip or conda, or …
9.6 Peak calling | Computational Genomics with R
Sep 9, 2008 · Peak calling is a statistical procedure, which uses coverage properties of ChIP and Input samples to find regions which are enriched due to protein binding. The procedure requires mapped reads, and outputs a set of …
ATAC-seq and gene regulatory network analysis - GitHub
RNA-seq data will be used to annotate peak regions exclusively to genes expressed in the condition analysed (during DiffBind differential accessibility analysis). If RNA_fastq_dirs is empty, peaks will be annotated using all genes …
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