Non-merged ChIP-Seq tracks summary (analysis)

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Revision as of 13:38, 17 June 2013 by BioUML wiki Bot (Talk | contribs)

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Analysis title
Default-analysis-icon.png Non-merged ChIP-Seq tracks summary
Provider
Institute of Systems Biology
Class
NonmergedChIPSeqSummary
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

Description

Summary of non-merged ChIP-Seq tracks (creation of tables: 'summaryOfTracks', 'summaryOfCellLines', 'summaryOfTfClasses', 'countsOfTfClassesInCellLines')

Parameters:

  • Sequences collection – Select a source of nucleotide sequences
    • Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
    • Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
  • Folder containing ChIP-seq tracks – Folder containing ChIP-seq tracks
  • Species – Select a taxonomical species
  • Cell line synonyms table – Cell line synonyms table (must contain the 'newNameOfCellLine' column)
  • TF names table – TF names table (TF class as a row name and TF title in 'tfName' column)
  • Path to output folder – Output folder will be created under this location
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