Tool stats & trends
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|Interface||Command line interface|
|Restrictions to use||None|
|Input format||BED, BAM, VCF, GFF|
|Output format||BED, BAM, VCF, GFF, BAI|
|License||GNU General Public License version 2.0|
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- person_outline Aaron R. Quinlan
Publication for BEDTools
Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes
[…] K4me1, and H3K27ac peaks were called using the MACS2 software package at false discovery rate (FDR) ≤ 1%. SICER was used to identify enriched domains for H3K27me3 and H3K9me3. For data visualization, BEDTools in combination with in-house scripts were used to generate normalized tag density profile at a window size of 200 bp and step size of 20 bp. We also visualized the average profile around TSS […]
Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width
[…] he -broad option. Default parameters for each of these methods were used. Generation of unions and intersections of the peak sets and quantification of reads mapped to peak regions was conducted with BEDTools using the commands bedtools merge, bedtools intersect, and bedtools coverage. Extended read coverage profiles were generated using MACS2 as described previously. Raw read coverage profiles we […]
The novel 19q13 KRAB zinc finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/β catenin signalling
[…] e. The GSM2424064_ENCFF191YCR_fold_change_over_control_GRCh38.bigWig file was downloaded. We annotated those peaks by using R package “CHIPseeker”. Subsequently, the gene region were intercepted with BEDTools and exported to Integrated Genomics Viewer software to map the peaks,. […]
Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects
[…] rdinates, and was therefore converted to 0-based coordinates to be consistent with the other three algorithms. We then annotated our catalog of circRNA candidates using UCSC RefSeq annotations  and BEDtools .The ratio of circular-to-linear RNA isoforms was calculated using the approach described in . For each circRNA candidate, we used the number of back-spliced reads for circRNA quantificat […]
NOTCH mediated non cell autonomous regulation of chromatin structure during senescence
[…] ty analysis compared to growing using the intersect of THOR and edgeR as described above. Regions displaying altered chromatin accessibility were mapped to genomic annotations or repeat regions using bedtools v2.26.0. For the genomic annotations, we used TSSs from the FANTOM database, repeats from repeatMasker (UCSC genome browser) and other genomic features (exons, introns, UTRs, etc.) were extra […]
Short genome report of cellulose producing commensal Escherichia coli 1094
[…] io reads using the single-end mode of Bwa mem v0.7.4  with default parameters (Fig. ). Output SAM files were converted to BAM files using SAMtools v0.1.19 . Sequencing coverage was computed using BEDtools v2.17.0 0  and values were normalized to 1 (genomes are haploids), from the median coverage over the large contigs (354×). The mapping coverage along the four PacBio contigs validated the s […]
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In comparison, however, Homer is better if you want to intersect further files because it gives more details, ideal to create a Venn diagram !
A big plus of bedtools : tools are very well documented, with schemes ! I like: "shuffle" to randomly relocate peaks, to test significance of a pathway enrichment for example !