Difference between revisions of "ChIPHorde (analysis)"

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==== Description ====
 
==== 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 http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_v3_manual.txt]
 
 
 
[[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 12:59, 27 June 2013

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

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