Difference between revisions of "ChIPHorde (analysis)"

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;Analysis title
 
;Analysis title
:[[File:ChIPMunk-ChIPHorde-icon.png]] ChIPHorde
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:[[File:Motif-discovery-ChIPHorde-icon.png]] ChIPHorde
 
;Provider
 
;Provider
 
:[[Autosome.Ru]]
 
:[[Autosome.Ru]]
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;Class
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:{{Class|biouml.plugins.chipmunk.ChipHordeAnalysis}}
 
;Plugin
 
;Plugin
:biouml.plugins.chipmunk (ChIPMunk plugin)
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:[[Biouml.plugins.chipmunk (plugin)|biouml.plugins.chipmunk (ChIPMunk plugin)]]
  
 
==== Description ====
 
==== Description ====
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* '''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-ChIPHorde-icon.png ChIPHorde
Provider
Autosome.Ru
Class
ChipHordeAnalysis
Plugin
biouml.plugins.chipmunk (ChIPMunk plugin)

[edit] Description

The ChIPHorde extension can be used to discover multiple significant motifs in a given dataset using two independent filtering strategies.

[edit] Parameters:

  • Input sequences – Collection containing input reads.
  • Start length – Start length of the matrix
  • Stop length – Stop length of the matrix
  • Motifs count limit – Maximum number of motifs to discover
  • Filtering mode – Whether to mask polyN ("Mask") or to drop entire sequence ("Filter")
  • 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 prefix – Prefix for the matrix name. It will be followed by number.

More about ChipHorde at: http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_v3_manual.txt

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