F-seq

F-seq is a software tool to estimate feature density using high-throughput sequence tags. The F-seq algorithmm produces continuous tag sequence density estimation that is useful, for example, to pinpoint egions of open chromatin in DNase-seq data or transcription factor binding sites in ChIP-seq data. The UCSC Genome Browser can display the F-seq output.

Topic

Sequencing;Sequence analysis

Detail

  • Operation: Peak calling

  • Software interface: Command-line user interface

  • Language: Java

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: -

  • Credit: National Science Foundation Graduate Research Fellowship, NIH.

  • Input: -

  • Output: -

  • Contact: Terrence S. Furey terry.furey@duke.edu, apboyle@umich.edu

  • Collection: -

  • Maturity: Stabel

Publications

  • F-Seq: a feature density estimator for high-throughput sequence tags.
  • Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8. doi: 10.1093/bioinformatics/btn480. Epub 2008 Sep 10. PMID: 18784119; PMCID: PMC2732284.
  • https://doi.org/10.1093/bioinformatics/btn480
  • PMID: 18784119
  • PMC: PMC2732284

Download and documentation

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