Difference between revisions of "DiChIPMunk (analysis)"

Latest revision as of 18:15, 9 December 2020

This analysis allows you to create di-nucleotide 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
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 – Name of created matrix

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:ChIPMunk-DiChIPMunk-icon.png]] DiChIPMunk
+:[[File:Motif-discovery-DiChIPMunk-icon.png]] DiChIPMunk
 ;Provider
 :[[Autosome.Ru]]
+;Class
+:{{Class|biouml.plugins.chipmunk.DiChipMunkAnalysis}}
+;Plugin
+:[[Biouml.plugins.chipmunk (plugin)|biouml.plugins.chipmunk (ChIPMunk plugin)]]
 ==== Description ====
@@ Line 13: / Line 17: @@
 * '''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)
+* '''Stop length''' – Stop length of the matrix
 * '''Number of threads''' (expert) – Number of concurrent threads when processing
 * '''Step limit''' (expert) – Step limit
@@ Line 27: / Line 31: @@
 [[Category:Analyses]]
-[[Category:ChIPMunk (analyses group)]]
+[[Category:Motif discovery (analyses group)]]
 [[Category:Autosome.Ru analyses]]
 [[Category:Autogenerated pages]]