bedtools shuffle (Chrom Tech)

About

News

Press Release

Team

Advisors

Partners

Contact

Bioz Stars

Bioz vStars

Buy from Supplier

Structured Review

Chrom Tech bedtools shuffle
Bedtools Shuffle, supplied by Chrom Tech, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bedtools/bedtools+shuffle/pmc13179062-359-5-7
Average 86 stars, based on 1 article reviews

bedtools shuffle - by Bioz Stars, 2026-11

86/100 stars

Images

other:

Article Title: Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots.
Article Snippet: BEDtools shuffle v2.30.0 (with parameter -chrom) was used to shuffle the TF ChIP-seq peaks associated with lincRNAs.

Article Title: Loss of DHX36/G4R1, a G4 resolvase, drives genome instability and regulates innate immune gene expression in cancer cells.
Article Snippet: To generate G4 random shuffle control, BEDTools (v. 2.27.1) shuffle was used to randomly choose genomic locations and keep features of G4 consensus sites on the same chromosome (-chrom).

Binding Assay:

Article Title: Integrative high-throughput enhancer surveying and functional verification divulges a YY2-condensed regulatory axis conferring risk for osteoporosis
Article Snippet: To explore whether predicted YY2 binding sites are significantly enriched in peak region of different epigenetic markers (inlcuding CTCF binding site) in osteoblasts or significant Hi-C chromatin interaction regions in hMSC differentiated osteoblast cells (Table S1), we randomly permuted genomic locations of predicted YY2 binding sites from DNase-seq peak regions in osteblasts using bedtools shuffle (-chrom -excl -noOverlapping) 1000 times.We then calculated counts of overlapped random locations against true locations for each feature using bedtools (v2.29.0). .. To explore whether predicted YY2 binding sites are significantly enriched in peak region of different epigenetic markers (inlcuding CTCF binding site) in osteoblasts or significant Hi-C chromatin interaction regions in hMSC differentiated osteoblast cells (Table S1), we randomly permuted genomic locations of predicted YY2 binding sites from DNase-seq peak regions in osteblasts using bedtools shuffle (-chrom -excl -noOverlapping) 1000 times.We then calculated counts of overlapped random locations against true locations for each feature using bedtools (v2.29.0). ..

Hi-C:

Preserving:

Article Title: Integrative Mapping of SNHG1 RNA-Chromatin Contacts onto the Cancer-Specific Super-Enhancer Landscape in HCT116 Colorectal Cancer Cells.
Article Snippet: .. In each of 1000 iterations, the 17,027 SNHG1 MACS2 peaks were shuffled across the genome using bedtools shuffle (-chrom -noOverlapping), preserving peak sizes and chromosomal assignment. ..

Generated:

Article Title: Epigenetic and transcriptomic alterations precede amyloidosis in the Alzheimer's disease App NL-G-F knock-in mouse model.
Article Snippet: .. These observed distances were then compared using the Wilcoxon signed-rank test to distances obtained against a randomly shuffled set of DMRs, generated by BEDtools shuffle (-chrom -noOverlapping)107. ..

Article Title: Satellite DNA fragility accompanies complex genome rearrangements and ecDNA oncogene amplification in canine osteosarcomas
Article Snippet: .. Randomized breakpoints were generated using bedtools shuffle with the following constraints: - Chromosome-preserving shuffling (-chrom) to maintain chromosome-level breakpoint density. ..

Article Title: Stranded short nascent strand sequencing reveals the topology of DNA replication origins in Trypanosoma brucei
Article Snippet: Violin plots were generated with the GraphPad Prism 8.3.0 software (RRID: SCR_002798 , GraphPad Software Inc, La Jolla, CA, USA). .. Shuffled controls were generated with bedtools shuffle (-chrom –noOverlapping –seed -excl) that randomly permutes genomic features provided respecting the number, the size, and chromosomal location and either excluding the detected origins or excluding detected origins and coding sequences (called intergenic shuffled control). ..

Control:

Insulation:

Article Title: Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.
Article Snippet: .. Bedtools shuffle (v2.31.1) (-chrom -noOverlapping) was used to generate a shuffled version of each set of breakpoints followed by two-tailed wilcoxon rank-sum tests to compare distance to nearest boundary, and minimum/median insulation score between observed and shuffled breakpoints. ..

Review