4Cseqpipe specifications

Information


Unique identifier OMICS_20367
Name 4Cseqpipe
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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4Cseqpipe in publications

 (6)
PMCID: 5479651
PMID: 28691095
DOI: 10.1126/sciadv.1700191

[…] dna (100 to 1000 bp) was selected for sequencing. different samples were pooled for sequencing using rapid mode on the hiseq 2500 system (illumina)., mapping of 4c data was carried out using 4cseqpipe algorithm, as previously described (). 4cseqpipe analyzes 4c-seq data by allowing sequence extraction, mapping, normalization, and plotting of cis-contact profiles. custom restriction site […]

PMCID: 5587731
PMID: 28549169
DOI: 10.1093/nar/gkx482

[…] libraries for each viewpoint are listed in supplementary table s1d., two independent 4c libraries were generated for each viewpoint in each cell type. the sequencing data were processed using the 4cseqpipe protocol (). all 4c-seq images were generated using default parameters of the pipeline., error bars denote standard error of the mean (sem). statistical significance was performed using […]

PMCID: 5116091
PMID: 27848966
DOI: 10.1038/ncomms13426

[…] interactions of the ormdl3 promoter ( and see methods)., genomic regions interacting with the ormdl3 promoter region were determined using two complementary analysis methods for 4c data (4c-ker and 4cseqpipe, see methods). we first pooled data from all risk and non-risk subjects and identified several interacting regions including the ctcf-bound regions near zbpb2 and ormdl3 gene loci, […]

PMCID: 4838340
PMID: 26673704
DOI: 10.1093/nar/gkv1358

[…] of libraries generated from same viewpoint in the same hi-seq flow cell. samples were sequenced on illumina hi-seq machines using standard protocols. the sequencing data were processed using the 4cseqpipe protocol (). all 4c-seq images were generated using default parameters of the pipeline., fish experiments were performed as described previously (). bacterial artificial chromosomes (bacs) […]

PMCID: 4381060
PMID: 25735743
DOI: 10.1093/nar/gkv144

[…] primer sequences were chosen to viewpoint sites, which were as close as possible to smc1/sa1 chip-seq peaks (supplementary table s7). 4c-seq data analysis and normalization was performed with 4cseqpipe () on the ncbi build 37 mouse genome assembly., pancreas from wild-type and sa1-heterozygous mice (five replicates corresponding to five individuals per genotype) were removed […]


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