Difference between revisions of "Cistrom construction (analysis)"

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(Automatic synchronization with BioUML)

Revision as of 18:14, 9 December 2020

Analysis title
Default-analysis-icon.png Cistrom construction
Provider
Institute of Systems Biology
Class
CistromConstruction
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

Description

Cistrom construction

Parameters:

  • Option – Please, select option (i.e. select the concrete session of given analysis).
  • Species – Please, select a taxonomical species
  • Path to folder with folders – Path to folder with folders (Each internal folder contains ChIP-seq tracks with peaks)
  • Folders names – Please, select folders names
  • Type of combined peaks – Please, select type of combined peaks
  • Minimal length of peaks – All peaks that are shorter than this threshold will be prolongated
  • Maximal length of peaks – All peaks that are longer than this threshold will be truncated
  • Do perform quality control? – Do perform quality control?
  • FPCM threshold – FPCM threshold
  • Site number threshold – If size of a data set is less than this threshold, then data set will be excluded from rank aggregation
  • Rank aggregation method – Please, select rank aggregation method
  • Parameters for OPTION_01 – Parameters for OPTION_01
    • Path to folder with cell lines – Path to folder with GTRD cell lines
    • Cell line – Please, select cell line.
    • Do remove cell treatments? – Do remove tracks when cell lines were treated?
  • Path to output folder – Path to output folder
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