Difference between revisions of "ChIPHorde (analysis)"

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(Automatic synchronization with BioUML)
(Automatic synchronization with BioUML)
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==== Description ====
 
==== Description ====
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The ChIPHorde extension can be used to discover multiple significant motifs in a given dataset using two independent filtering strategies.
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==== Parameters: ====
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* '''Input sequences''' – Collection containing input reads.
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* '''Start length''' – Start length of the matrix
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* '''Stop length''' – Stop length of the matrix
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* '''Motifs count limit''' – Maximum number of motifs to discover
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* '''Filtering mode''' – Whether to mask polyN ("Mask") or to drop entire sequence ("Filter")
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* '''Number of threads''' (expert) – Number of concurrent threads when processing
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* '''Step limit''' (expert) – Step limit
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* '''Try limit''' (expert) – Try limit
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* '''GC percent''' (expert) – Fraction of GC nucleotides (0..1), set to -1 for auto
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* '''ZOOPS factor''' (expert) – Zero-or-one-occurence-per-sequence factor
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* '''Motif shape''' (expert) – Motif shape
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* '''Use peak profiles''' (expert) – Whether to use peak profiles (if available)
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* '''Output matrix library''' – Path to the matrix library to put matrix into (will be created if not specified)
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* '''Matrix name prefix''' – Prefix for the matrix name. It will be followed by number.
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More about ChipHorde at: [http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_v3_manual.txt http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_v3_manual.txt]
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[[Category:Analyses]]
 
[[Category:Analyses]]
 
[[Category:ChIPMunk (analyses group)]]
 
[[Category:ChIPMunk (analyses group)]]
 
[[Category:Autosome.Ru analyses]]
 
[[Category:Autosome.Ru analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Revision as of 13:17, 27 June 2013

Analysis title
ChIPMunk-ChIPHorde-icon.png ChIPHorde
Provider
Autosome.Ru
Class
ChipHordeAnalysis
Plugin
biouml.plugins.chipmunk (ChIPMunk plugin)

Description

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

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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