BEDTools: the Swiss-army tool for genome feature analysis

By A. Quinlan. Current Protocols in Bioinformatics, 2014

2,219 citations recorded by the source corpus.

Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse cellular phenomena such as gene isoform expression and transcription factor binding. Extracting biological insight from the experiments enabled by these advances demands the analysis of large, multi‐dimensional datasets. This unit describes the use of the BEDTools toolkit for the exploration of high‐throughput genomics datasets. Several protocols are presented for common genomic analyses, demonstrating how simple BEDTools operations may be combined to create bespoke pipelines addressing complex questions. Curr. Protoc. Bioinform. 47:11.12.1‐11.12.34. © 2014 by John Wiley & Sons, Inc.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2e9678c7f0d2d35b8b5b7740c2f6891665b06bf1

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Citations in the corpus

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore (2020, methodology): “The ground truth was assigned for each readset using bedtools intersect [30] with the options -F 1.”
ipyrad: Interactive assembly and analysis of RADseq datasets (2020, methodology): “…written in Python, it retains high performance through the use of just-in-time compilation (Lam et al., 2015), and incorporation of industry standard compiled software into the assembly pipeline (Edgar, 2004; Li et al., 2009; Li and Durbin, 2009; Martin, 2011; Quinlan, 2014; Rognes et al., 2016).”
Organization of Chromatin by Intrinsic and Regulated Phase Separation (2019, methodology): “Mouse nucleosome positions were converted to the mm10 build of genome using CrossMap (Zhao et al., 2014), and internucleosome distances (140–250 bp) were determined using Bedtools (Quinlan, 2014; Quinlan and Hall, 2010).”
Mosdepth: quick coverage calculation for genomes and exomes (2017, background): “Samtools depth (Li et al. , 2009) outputs per-base coverage; BEDTools genomecov (Quinlan and Hall, 2010; Quinlan, 2014) can output per-region or per-base coverage; Sambamba (Tarasov et al. , 2015) also provides per-base and per-window depth calculations.”
Non-coding RNA analysis using the Rfam database (2018, methodology): “' > my.cmscan.gff The my.cmscan.gff ﬁle can then be used as input to a program for identifying overlaps between two datasets, such as the bedtools intersect program (Quinlan, 2014).”