Difference between revisions of "ChIPMunk (analysis)"

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Revision as of 15:24, 4 April 2013

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

It identifies the motif with the maximum Discrete Information Content in a set of DNA sequences. ChIPMunk uses (extended) multifasta as the input format and supports IUPAC DNA letters in the input sequences.

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)
  • 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 – Name of created matrix

More about ChIPMunk at: http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_details.rhtml

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