Difference between revisions of "ChIPMunk (analysis)"

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;Analysis title
 
;Analysis title
:ChIPMunk
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:[[File:Motif-discovery-ChIPMunk-icon.png]] ChIPMunk
 
;Provider
 
;Provider
 
:[[Autosome.Ru]]
 
:[[Autosome.Ru]]
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;Class
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:{{Class|biouml.plugins.chipmunk.ChipMunkAnalysis}}
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;Plugin
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:[[Biouml.plugins.chipmunk (plugin)|biouml.plugins.chipmunk (ChIPMunk plugin)]]
  
 
==== Description ====
 
==== Description ====
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* '''Input sequences''' – Collection containing input reads.
 
* '''Input sequences''' – Collection containing input reads.
 
* '''Start length''' – Start length of the matrix
 
* '''Start length''' – Start length of the matrix
* '''Stop length''' – Stop length of the matrix (less or equal than start length)
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* '''Stop length''' – Stop length of the matrix
 
* '''Number of threads''' (expert) – Number of concurrent threads when processing
 
* '''Number of threads''' (expert) – Number of concurrent threads when processing
 
* '''Step limit''' (expert) – Step limit
 
* '''Step limit''' (expert) – Step limit
 
* '''Try limit''' (expert) – Try limit
 
* '''Try limit''' (expert) – Try limit
* '''GC percent''' (expert) – Fraction of GC nucleotides (0..1)
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* '''GC percent''' (expert) – Fraction of GC nucleotides (0..1), set to -1 for auto
 
* '''ZOOPS factor''' (expert) – Zero-or-one-occurence-per-sequence factor
 
* '''ZOOPS factor''' (expert) – Zero-or-one-occurence-per-sequence factor
 
* '''Motif shape''' (expert) – Motif shape
 
* '''Motif shape''' (expert) – Motif shape
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[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:ChIPMunk (analyses group)]]
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[[Category:Motif discovery (analyses group)]]
 
[[Category:Autosome.Ru analyses]]
 
[[Category:Autosome.Ru analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:15, 9 December 2020

Analysis title
Motif-discovery-ChIPMunk-icon.png ChIPMunk
Provider
Autosome.Ru
Class
ChipMunkAnalysis
Plugin
biouml.plugins.chipmunk (ChIPMunk plugin)

[edit] Description

This analysis allows you to create motifs from Chip-Seq data.

It identifies the motif with the maximum Discrete Information Content in a set of DNA sequences.

[edit] Parameters:

  • Input sequences – Collection containing input reads.
  • Start length – Start length of the matrix
  • Stop length – Stop length of the matrix
  • Number of threads (expert) – Number of concurrent threads when processing
  • Step limit (expert) – Step limit
  • Try limit (expert) – Try limit
  • GC percent (expert) – Fraction of GC nucleotides (0..1), set to -1 for auto
  • ZOOPS factor (expert) – Zero-or-one-occurence-per-sequence factor
  • Motif shape (expert) – Motif shape
  • Use peak profiles (expert) – Whether to use peak profiles (if available)
  • Output matrix library – Path to the matrix library to put matrix into (will be created if not specified)
  • Matrix name – Name of created matrix

More about ChIPMunk at: http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_details.rhtml

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