Difference between revisions of "GTRD analysis advanced (analysis)"

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(Automatic synchronization with BioUML)
 
(Automatic synchronization with BioUML)
 
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==== Parameters: ====
 
==== Parameters: ====
  
−
* '''Option''' – Select option (the concrete session of given analysis).
+
* '''Option''' – Select option (Select the concrete session of given analysis).
 
* '''Parameters for OPTION_01''' – Please, determine parameters for OPTION_01
 
* '''Parameters for OPTION_01''' – Please, determine parameters for OPTION_01
 
** '''Species''' – Select a taxonomical species
 
** '''Species''' – Select a taxonomical species
 
** '''Path to folder with folders''' – Path to folder with folders (that contain (ChIP-seq) tracks)
 
** '''Path to folder with folders''' – Path to folder with folders (that contain (ChIP-seq) tracks)
 
** '''Folders names''' – Select folders names
 
** '''Folders names''' – Select folders names
−
** '''Minimal length of site''' – Minimal length of site (or binding region)
+
** '''Path to folder with matrices''' – Path to folder with frequency matrices
−
** '''Maximal length of site''' – Maximal length of site (or binding region)
+
 
* '''Parameters for OPTION_2''' – Please, determine parameters for OPTION_02
 
* '''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)
 
** '''Path to folder with folders''' – Path to folder with folders (that contain (ChIP-seq) tracks)
 
** '''Folders names''' – Select folders names
 
** '''Folders names''' – Select folders names
−
** '''Path to folder with matrices''' – Path to folder with frequency matrices
+
* '''Parameters for OPTION_3''' – Please, determine parameters for OPTION_03
−
* '''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 <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
+
−
*** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> 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)
 
** '''Path to folder with folders''' – Path to folder with folders (that contain (ChIP-seq) tracks)
 
** '''Folders names''' – Select folders names
 
** '''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
 
* '''Path to output folder''' – Path to output folder
  

Latest revision as of 18:14, 9 December 2020

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

[edit] Description

Analysis of GTRD peaks

[edit] Parameters:

  • Option – Select option (Select 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
    • Path to folder with matrices – Path to folder with frequency matrices
  • Parameters for OPTION_2 – Please, determine parameters for OPTION_02
    • Path to folder with folders – Path to folder with folders (that contain (ChIP-seq) tracks)
    • Folders names – Select folders names
  • Parameters for OPTION_3 – Please, determine parameters for OPTION_03
    • Path to folder with folders – Path to folder with folders (that contain (ChIP-seq) tracks)
    • Folders names – Select folders names
  • Path to output folder – Path to output folder
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