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F-Seq

A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

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1 user review

1 user review

Fabien Pichon's avatar image Fabien Pichon's country flag

Fabien Pichon

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 !

F-Seq forum

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F-Seq classification

F-Seq specifications

Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable

F-Seq distribution

versioning

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No versioning.

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Publications

Institution(s)

Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA

Link to literature

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