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 ChIP-seq track (must be the result of MACS or SISSRs analysis)
+
* '''Input track''' – Select input track (it can be ChIP-seq track from GTRD; thus, it can be the result of MACS or SISSRs peak-finder)
 
* '''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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* '''Is around summit''' – Is around summit
 
* '''Is around summit''' – Is around summit
 
* '''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 frequency matrix
 
* '''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 when it doesn<nowiki>'</nowiki>t exist
 
* '''Path to output folder''' – Output folder will be created under this location when it doesn<nowiki>'</nowiki>t exist

Latest revision as of 19:00, 13 February 2017

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)

[edit] Description

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

[edit] Parameters:

  • Input track – Select input track (it can be ChIP-seq track from GTRD; thus, it can be the result of MACS or SISSRs peak-finder)
  • 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 frequency matrix
  • Types of site models – Select site models for comparative analysis
  • Path to output folder – Output folder will be created under this location when it doesn't exist
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