Difference between revisions of "ChIPMunk (analysis)"

Latest revision as of 18:15, 9 December 2020

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
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 – Name of created matrix

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:ChIPMunk-ChIPMunk-icon.png]] ChIPMunk
+:[[File:Motif-discovery-ChIPMunk-icon.png]] ChIPMunk
 ;Provider
 :[[Autosome.Ru]]
+;Class
+:{{Class|biouml.plugins.chipmunk.ChipMunkAnalysis}}
 ;Plugin
 :[[Biouml.plugins.chipmunk (plugin)|biouml.plugins.chipmunk (ChIPMunk plugin)]]
@@ Line 19: / Line 21: @@
 * '''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
@@ Line 29: / Line 31: @@
 [[Category:Analyses]]
-[[Category:ChIPMunk (analyses group)]]
+[[Category:Motif discovery (analyses group)]]
 [[Category:Autosome.Ru analyses]]
 [[Category:Autogenerated pages]]