Difference between revisions of "ChIPMunk (analysis)"
From BioUML platform
m (Protected "ChIPMunk (analysis)": Autogenerated page ([edit=sysop] (indefinite))) |
(Automatic synchronization with BioUML) |
||
| Line 13: | Line 13: | ||
* '''GC percent''' (expert) – Fraction of GC nucleotides (0..1) | * '''GC percent''' (expert) – Fraction of GC nucleotides (0..1) | ||
* '''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 | ||
* '''Use peak profiles''' (expert) – Whether to use peak profiles (if available) | * '''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) | * '''Output matrix library''' – Path to the matrix library to put matrix into (will be created if not specified) | ||
| Line 20: | Line 21: | ||
[[Category:Analyses]] | [[Category:Analyses]] | ||
| − | [[Category: | + | [[Category:ChIPMunk (analyses group)]] |
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Revision as of 18:12, 12 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. ChIPMunk uses (extended) multifasta as the input format and supports IUPAC DNA letters in the input sequences.
Parameters:
- 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
More about ChIPMunk at: http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_details.rhtml
