Difference between revisions of "ChIPHorde (analysis)"

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Revision as of 15:24, 4 April 2013

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 (less or equal than start length)
  • 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)
  • ZOOPS factor (expert) – Zero-or-one-occurence-per-sequence factor
  • 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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