GTRD analysis advanced (analysis)

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

Description

Analysis of GTRD peaks

Parameters:

  • Option – Select option (the concrete session of given analysis).
  • Parameters for OPTION_01 – Please, determine parameters for OPTION_01
    • Species – Select a taxonomical species
    • Path to folder with folders – Path to folder with folders (that contain (ChIP-seq) tracks)
    • Folders names – Select folders names
    • Minimal length of site – Minimal length of site (or binding region)
    • Maximal length of site – Maximal length of site (or binding region)
  • Parameters for OPTION_2 – Please, determine parameters for OPTION_02
    • Species – Select a taxonomical species
    • Path to folder with tracks – Path to folder with (ChIP-seq) tracks
    • Minimal length of site – Minimal length of site (or binding region)
    • Maximal length of site – Maximal length of site (or binding region)
  • Parameters for OPTION_3 – Please, determine parameters for OPTION_03
    • Path to folder with files – Path to folder with files
  • Parameters for OPTION_04 – Please, determine parameters for OPTION_04
    • Species – Select a taxonomical species
    • Path to folder with folders – Path to folder with folders (that contain (ChIP-seq) tracks)
    • Folders names – Select folders names
    • Path to folder with matrices – Path to folder with frequency matrices
  • Parameters for OPTION_05 – Please, determine parameters for OPTION_05
    • 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
    • Path to folder with files – Path to folder with files
    • Path to folder with matrices – Path to folder with frequency matrices
    • Path to folder with site models – Path to folder with site models
    • Path to input table – Path to input table
  • Parameters for OPTION_06 – Please, determine parameters for OPTION_06
    • Path to folder with files – Path to folder with files
    • Do remove orphans – Do remove orphans
    • Path to input table – Path to input table
  • Parameters for OPTION_07 – Please, determine parameters for OPTION_07
    • Path to folder with folders – Path to folder with folders (that contain (ChIP-seq) tracks)
    • Folders names – Select folders names
    • Path to input table – Path to input table
  • Parameters for OPTION_08 – Please, determine parameters for OPTION_08
    • Path to folder with files – Path to folder with files
    • Do track (or table)? – Do write sites into track (or table)?
  • Path to output folder – Path to output folder
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