Difference between revisions of "ChIPMunk (analysis)"

Revision as of 14:00, 16 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.

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

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