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Protocols

fourSig specifications

Information


Unique identifier OMICS_02628
Name fourSig
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Terry Magnuson

Publication for fourSig

fourSig citations

 (7)
call_split

Genome wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys

2018
Genome Biol
PMCID: 5806489
PMID: 29422066
DOI: 10.1186/s13059-018-1390-8
call_split See protocol

[…] rimer were selected from the total fastq file. The selected reads were mapped to the mm9 assembly with Bowtie2 (version 2.2.2). The mapped reads were further mapped to HindIII sites with the software fourSig []. The fragment counts were finally normalized per one million reads. […]

library_books

A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers

2017
Sci Rep
PMCID: 5645309
PMID: 29042628
DOI: 10.1038/s41598-017-13748-8

[…] .uk/projects/fastqc/).Reads with a minimum length of 30 bp were mapped to the mm10 reference genome using Bowtie1, allowing 0 mismatches. Mapped reads were assigned to DpnII digestion fragments using fourSig. The following reads were removed from the files: 1) self-ligated reads, 2) uncut reads (fragments adjacent to baits), and 3) reads at fragments that have at least 1 read in the control (non-l […]

library_books

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

2016
Mol Syst Biol
PMCID: 5199122
PMID: 27940490
DOI: 10.15252/msb.20167311

[…] Trimmed reads were then mapped to the reference genome (hg19) using the short read aligner BWA‐MEM (Li & Durbin, ; exact parameters were as follows: BWA MEM ‐t 8 ‐k 15 ‐r 1 ‐B 1 –M) and processed via fourSig or FourCSeq. Data were then visualized by uploading. BedGraph files to the UCSC genome browser (https://genome.ucsc.edu/; hg19) and using its embedded smoothing option. i4C‐seq replicates and […]

call_split

Long noncoding RNA TUG1 is downregulated in non small cell lung cancer and can regulate CELF1 on binding to PRC2

2016
BMC Cancer
PMCID: 4971684
PMID: 27485439
DOI: 10.1186/s12885-016-2569-6
call_split See protocol

[…] tool for aligning sequencing reads against reference sequences []. Bowtie2 was used to align unknown fragments against human genome sequences (Grch38.p2 was used in the present study). Subsequently, fourSig, a software suite for analyzing and visualizing 4C-seq data, was used to identify the potential TUG1 interactive regions []. The command “bamToReTab.pl –H 210 500 300 bowtie2_output hind3_site […]

library_books

Long Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression

2016
PLoS Genet
PMCID: 4852938
PMID: 27135601
DOI: 10.1371/journal.pgen.1005992

[…] mosome of the bait were kept and assigned the HindIII restricted fragments defined by two neighboring restriction sites. Peak calling was performed with a custom-designed pipeline generally following FourSig []. Previous interactome studies reported that 99% interactions were less than 1 Mb and inter-chromosomal interactions were hard to be validated []. Hence, we only considered intra-interaction […]

library_books

Chromatin interactions and candidate genes at ten prostate cancer risk loci

2016
Sci Rep
PMCID: 4793270
PMID: 26979803
DOI: 10.1038/srep23202

[…] all probes. The probes which were located in repeat sequences or had low capture efficiency (lower 22 percentile) were removed. The significant interactions at each probe region were determined using fourSig software. […]

Citations

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fourSig institution(s)
Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
fourSig funding source(s)
National Institutes of Health (NIH) [R01GM10974, NIH F32-CA144389]

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