F-Seq protocols

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F-Seq specifications

Information


Unique identifier OMICS_00482
Name F-Seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Terrence Furey <>

Publication for F-Seq

F-Seq in pipelines

 (6)
2018
PMCID: 5886697
PMID: 29579120
DOI: 10.1371/journal.ppat.1006954

[…] and hsv-1 genomes was performed as described for the 4su-seq data. bam files with mapped reads were converted to bed format using bedtools [] and ocrs were determined from these bed files using f-seq with default parameters []. no filtering of ocrs was performed. assignment of ocrs to gene promoters was performed using chipseeker []. 5kb docr length for each gene was calculated […]

2017
PMCID: 5509746
PMID: 28706189
DOI: 10.1038/s41598-017-05349-2

[…] to exclude improperly paired reads and pcr duplicates. wiggle tracks were generated for visualization on the ucsc genome browser., to identify accessible chromatin “peaks” from faire-seq reads, f-seq was used with default parameters and a 250 bp feature length. irreproducible discovery rate (idr) analysis was then used to find reproducible peaks between two replicates. a union set of peaks […]

2017
PMCID: 5511350
PMID: 28703137
DOI: 10.1038/ncomms16058

[…] using the triweight smoothing method. bedgraph files were converted to bigwig using bedgraphtobigwig (https://www.encodeproject.org/software/bedgraphtobigwig). open chromatin peaks were called with f-seq with fragment size (-f) at 0 and the ‘s.d. threshold’ (-t) at 6. we removed peaks overlapping encode blacklisted regions (https://www.encodeproject.org/annotations/encsr636hff/) using bedtools […]

2016
PMCID: 4824487
PMID: 27055116
DOI: 10.1371/journal.pgen.1005893

[…] public download repository at http://genome.ucsc.edu/encode/downloads.html. the peak call for the identification of regions in which aligned reads were significantly enriched was implemented via f-seq version 1.84 with the use of background model for 20 bp sequences []., endometrial carcinoma cell lines (hec251 [jcrb1141] and hec265 [jcrb1142]) were grown in dmem (sigma-aldrich) with 10% […]

2013
PMCID: 3572043
PMID: 23418607
DOI: 10.1371/journal.pone.0056842

[…] reference rdna. in this study, unique reads refer to different types of reads, and redundant reads refer to total reads., the abundance distribution of srrnas in rdna unit was analyzed by f-seq 1.0 . the top 20 abundantly expressed srrnas were selected according to their average abundance in the two indicated samples. to compare the srrna expression level in normal and diabetic […]


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F-Seq in publications

 (64)
PMCID: 5859501
PMID: 29558892
DOI: 10.1186/s12864-018-4542-z

[…] then used to convert the bam output into bed format. the bed files were loaded into fseq (v1.85) [] to call peaks using parameters -f 0 and -t 2, where -t 2 is a sensitive peak detection threshold. f-seq has been shown to be a sensitive and accurate peak caller for dnase-seq and atac-seq data []. the fraction of reads within peaks (the frip score) was calculated using bedtools by extracting […]

PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003

[…] the comparison of mnase-seq datasets and the identification of dynamic nucleosomes that respond to environmental conditions and development stages., for dnase-seq data analyses, algorithms such as f-seq [] and hotspot [,] are specifically designed to manage the unique features of dnase-seq data. f-seq implements a smooth gaussian kernel density estimation and has been implemented […]

PMCID: 5813008
PMID: 29445214
DOI: 10.1038/s41598-018-21460-4

[…] .5 µl of es, 1 µl of primer rack1_r_seq (1 pmol) and 3.5 µl of rna template. the pcr reaction was carried out in 25 µl reaction, containing 12.5 µl of 2× transhifi supermix ii, 0.5 µl of primer rack1_f_seq (0.1 pmol), 0.5 µl of primer rack1_r_seq (0.1 pmol), 1 µl of cdna template (about 400 ng) and 10.5 µl of water. the amplification program was 94 °c for 5 min and 35 cycles of 94 °c for 30 s, 60  […]

PMCID: 5703546
PMID: 29176792
DOI: 10.1371/journal.pone.0188056

[…] using bowtie (version 1.1.2) allowing up to two base mismatches. dnase-seq analyses were confirmed by two biological replicates, each constituting technical duplicates on significant peaks called by f-seq [] using a standard deviation threshold value of 4. normalized signal tracks were generated using align2rawsignal (kundaje a., http://code.google.com/p/align2rawsignal/) on combined bam files […]

PMCID: 5701797
PMID: 29246318
DOI: 10.1016/j.omtn.2017.10.010

[…] or were excluded from macrophage engulfment., to demonstrate increased cellular binding of rna nanoparticles compared with small ssrna, we incubated both cy3-labeled 2′f sqr-seq (50 nm) and 2′f seq (200 nm) with macrophage-like raw 264.7 cells at equimolar concentration of seq and evaluated them by confocal microscopy. co-localization of the cy3 signal (red) and cellular actin (green) […]


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F-Seq institution(s)
Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
F-Seq funding source(s)
Supported by National Science Foundation Graduate Research Fellowship and NIH Grants HG004563 and HG003169.

F-Seq review

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Fabien Pichon

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Desktop
Used for FAIRE-seq. Usefull for noisy data, but a little bit complex to use, but still less complex than ZINBA. You have to generate background .bff files with the help of GEM tools and convert .mappability file into .wig file, but .iff files are more obscure. Fortunately, Furey's lab provided some generic ones. Nonetheless I never could reproduce exactly their peak calling using ENCODE data... it seems there is a part of randomness in the process. Also, note that you need an additionnal perl script to calculate peaks p-values !