Difference between revisions of "ChIPMunk (analysis)"
From BioUML platform
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* '''Step limit''' (expert) – Step limit | * '''Step limit''' (expert) – Step limit | ||
* '''Try limit''' (expert) – Try 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 | * '''ZOOPS factor''' (expert) – Zero-or-one-occurence-per-sequence factor | ||
* '''Motif shape''' (expert) – Motif shape | * '''Motif shape''' (expert) – Motif shape | ||
Revision as of 11:27, 24 May 2013
- Analysis title
ChIPMunk
- Provider
- Autosome.Ru
- Plugin
- biouml.plugins.chipmunk (ChIPMunk plugin)
Description
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.
Parameters:
- 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
More about ChIPMunk at: http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_details.rhtml
