Difference between revisions of "ChIPHorde (analysis)"

Revision as of 11:27, 24 May 2013

The ChIPHorde extension can be used to discover multiple significant motifs in a given dataset using two independent filtering strategies.

Input sequences – Collection containing input reads.
Start length – Start length of the matrix
Stop length – Stop length of the matrix
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), set to -1 for auto
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.

@@ Line 19: / Line 19: @@
 * '''Step limit''' (expert) – Step limit
 * '''Try limit''' (expert) – Try limit
-* '''GC percent''' (expert) – Fraction of GC nucleotides (0..1)
+* '''GC percent''' (expert) – Fraction of GC nucleotides (0..1), set to -1 for auto
 * '''ZOOPS factor''' (expert) – Zero-or-one-occurence-per-sequence factor
 * '''Motif shape''' (expert) – Motif shape