F-Seq specifications

Unique identifier:
OMICS_00482
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes

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Publications

Institution(s)

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

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1 user review

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

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 !