Difference between revisions of "Correlations of best sites (analysis)"

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(Automatic synchronization with BioUML)
(Automatic synchronization with BioUML)
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==== Parameters: ====
 
==== Parameters: ====
  
* '''Input track''' – Select input peaks track (must be the result of MACS or SISSRs analysis)
+
* '''Input track''' – Select input ChIP-seq track (must be the result of MACS or SISSRs analysis)
 
* '''Sequences collection''' – Select a source of nucleotide sequences
 
* '''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
 
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
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* '''Minimal region length''' – Minimal length of sequence region
 
* '''Minimal region length''' – Minimal length of sequence region
 
* '''Matrix''' – Path to positional weight matrix
 
* '''Matrix''' – Path to positional weight matrix
* '''Output table path''' – Path to the output table
 
 
* '''Types of site models''' – Select site models for comparative analysis
 
* '''Types of site models''' – Select site models for comparative analysis
 +
* '''Path to output folder''' – Output folder will be created under this location
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]

Revision as of 16:17, 11 December 2014

Analysis title
Default-analysis-icon.png Correlations of best sites
Provider
Institute of Systems Biology
Class
BestSiteCorrelations
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

Description

Best sites: correlation between best sites and characteristics of single chip-seq track; summit(yes/no)

Parameters:

  • Input track – Select input ChIP-seq track (must be the result of MACS or SISSRs analysis)
  • 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
  • Is around summit – Is around summit
  • Minimal region length – Minimal length of sequence region
  • Matrix – Path to positional weight matrix
  • Types of site models – Select site models for comparative analysis
  • Path to output folder – Output folder will be created under this location
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