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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

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Maintainer


  • person_outline Terry Magnuson <>

Publication for fourSig

fourSig in publications

 (7)
PMCID: 5806489
PMID: 29422066
DOI: 10.1186/s13059-018-1390-8

[…] 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., dmvs were identified as previously described []. briefly, the genome was first divided into 1-kb bins, and the dna […]

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

[…] 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 […]

PMCID: 5199122
PMID: 27940490
DOI: 10.15252/msb.20167311

[…] by the samd4a tss by inverse pcr, and amplimer sequencing. in parallel, the same viewpoint and primers were used to generate conventional 4c profiles. the resulting data were processed via “foursig” (williams et al, ) to correct for mapping biases and identify significant interactions. comparison of i4c and conventional 4c samd4a cis‐interactions revealed extensive similarities, […]

PMCID: 4971684
PMID: 27485439
DOI: 10.1186/s12885-016-2569-6

[…] 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 […]

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

[…] 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 […]


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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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