DiChIPMunk (analysis)

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

Description

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

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

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
  • Local background (expert) – If checked, local background estimation is used. Otherwise uniform background estimation is used
  • 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 DiChIPMunk at: http://autosome.ru/dichipmunk/

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