GTRD analysis

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Analysis title
Default-analysis-icon.png GTRD analysis
Provider
Institute of Systems Biology
Class
GtrdAnalysis
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
    • 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
    • Species – Select a taxonomical species
    • Path to folder with tracks – Path to folder with (ChIP-seq) tracks
    • Track size threshold – Track size threshold
    • Path to input table – Path to input table
    • Name of column for chromosome names – Select name of the table column for chromosome names
    • Name of column for TSS positions – Select name of the table column for TSS positions
    • Name of {'+', '-'}-column for TSS strands – Select name of the table column for TSS strands
    • Promoter regions – Promoter regions
  • Parameters for OPTION_2 – Please, determine parameters for OPTION_02
    • Path to folder with tracks – Path to folder with (ChIP-seq) tracks
    • Path to folder with files – Path to folder with files that contain coverage matrices
  • Parameters for OPTION_03 – Please, determine parameters for OPTION_03
    • Species – Select a taxonomical species
    • Path to folder with tracks – Path to folder with (ChIP-seq) tracks
  • Parameters for OPTION_04 – Please, determine parameters for OPTION_04
    • Path to folder with tracks – Path to folder with (ChIP-seq) tracks
    • Tracks names – Select tracks 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_05 – Please, determine parameters for OPTION_05
    • 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_06 – Please, determine parameters for OPTION_06
    • 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_07 – Please, determine parameters for OPTION_07
    • 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 input table – Path to input table
    • Path to folder with matrices – Path to folder with frequency matrices
    • Site model type – Select site model type
    • Path to folder with tables – Path to folder with tables
    • Do remove orphans – Do remove orphans
    • Do extract random regions – Do extract random regions
    • Minimal number of regions – Minimal number of regions
  • Parameters for OPTION_08 – Please, determine parameters for OPTION_08
    • 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 input table – Path to input table
    • Path to folder with matrices – Path to folder with frequency matrices
  • Parameters for OPTION_09 – Please, determine parameters for OPTION_09
    • 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 input table – Path to input table
    • Path to folder with matrices – Path to folder with frequency matrices
    • Path to folder with tables – Path to folder with tables
    • Do remove orphans – Do remove orphans
    • Minimal number of regions – Minimal number of regions
  • Path to output folder – Path to output folder
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