F-Seq pipeline

F-Seq specifications


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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  • person_outline Terrence Furey <>

Publication for F-Seq

F-Seq citation

PMCID: 5703546

[…] 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 [25] 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 […]

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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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 !