Difference between revisions of "DiChIPHorde (analysis)"

Revision as of 14:07, 16 April 2013

The DiChIPHorde extension can be used to discover multiple significant di-nucleotide 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
• 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 prefix – Prefix for the matrix name. It will be followed by number.

More about DiChIPMunk at: http://autosome.ru/dichipmunk/