GTRD analysis

Analysis title

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