F-Seq statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool F-Seq
info

Tool usage distribution map

This map represents all the scientific publications referring to F-Seq per scientific context
info info

Associated diseases

This word cloud represents F-Seq usage per disease context
info

Popular tool citations

chevron_left Peak calling Nucleosome positioning chevron_right
Want to access the full stats & trends on this tool?

Protocols

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

Download


download.png
github.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Terrence Furey

Publication for F-Seq

F-Seq citations

 (50)
library_books

Global analysis of primary mesenchyme cell cis regulatory modules by chromatin accessibility profiling

2018
BMC Genomics
PMCID: 5859501
PMID: 29558892
DOI: 10.1186/s12864-018-4542-z

[…] s 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 and […]

call_split

Computational Methods for Assessing Chromatin Hierarchy

2018
Comput Struct Biotechnol J
PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003
call_split See protocol

[…] 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 in combination […]

library_books

Genome wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre osteoblast differentiation

2017
PLoS One
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 of […]

library_books

Variation in DNA Damage Responses to an Inhalational Carcinogen (1,3 Butadiene) in Relation to Strain Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice

2017
Environ Health Perspect
PMCID: 5944832
PMID: 29038090
DOI: 10.1289/EHP1937

[…] etaPrior set to “false.” For miRNAs, a minimum threshold of 10 reads in at least five mice from one strain was required.For accessible regions, the union set of the top 50,000 peaks, as determined by F-seq (), from all samples was identified. The number of mapped reads within 300-bp overlapping windows (peaks smaller than 300bp were expanded to 300 bp) within peaks was computed for each sample (32 […]

library_books

Correcting nucleotide specific biases in high throughput sequencing data

2017
BMC Bioinformatics
PMCID: 5540620
PMID: 28764645
DOI: 10.1186/s12859-017-1766-x

[…] positive and negative groups are used to compute ROC curves and AUC values (Additional file : Table S1).We identified open chromatin peaks in DNase-seq, ATAC-seq, FAIRE-seq, and ChIP-seq peaks using F-seq []. For each experimental dataset, we merged the BAM files for all independently bias-corrected replicates, then F-seq was run with the default parameters, outputting peaks in BED format. To run […]

library_books

Platelet function is modified by common sequence variation in megakaryocyte super enhancers

2017
Nat Commun
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 v […]


Want to access the full list of citations?
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

star_border star_border star_border star_border star_border
star star star star star

Fabien Pichon

star_border star_border star_border star_border star_border
star star star star star
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 !