ChIPMunk (analysis)

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