Difference between revisions of "ChIPHorde (analysis)"
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;Analysis title | ;Analysis title | ||
| − | :ChIPHorde | + | :[[File:Motif-discovery-ChIPHorde-icon.png]] ChIPHorde |
;Provider | ;Provider | ||
:[[Autosome.Ru]] | :[[Autosome.Ru]] | ||
| + | ;Class | ||
| + | :{{Class|biouml.plugins.chipmunk.ChipHordeAnalysis}} | ||
| + | ;Plugin | ||
| + | :[[Biouml.plugins.chipmunk (plugin)|biouml.plugins.chipmunk (ChIPMunk plugin)]] | ||
==== Description ==== | ==== Description ==== | ||
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* '''Input sequences''' – Collection containing input reads. | * '''Input sequences''' – Collection containing input reads. | ||
* '''Start length''' – Start length of the matrix | * '''Start length''' – Start length of the matrix | ||
| − | * '''Stop length''' – Stop length of the matrix | + | * '''Stop length''' – Stop length of the matrix |
* '''Motifs count limit''' – Maximum number of motifs to discover | * '''Motifs count limit''' – Maximum number of motifs to discover | ||
* '''Filtering mode''' – Whether to mask polyN ("Mask") or to drop entire sequence ("Filter") | * '''Filtering mode''' – Whether to mask polyN ("Mask") or to drop entire sequence ("Filter") | ||
| Line 17: | Line 21: | ||
* '''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 | ||
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[[Category:Analyses]] | [[Category:Analyses]] | ||
| − | [[Category: | + | [[Category:Motif discovery (analyses group)]] |
[[Category:Autosome.Ru analyses]] | [[Category:Autosome.Ru analyses]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Latest revision as of 18:15, 9 December 2020
- Analysis title
ChIPHorde
- Provider
- Autosome.Ru
- Class
ChipHordeAnalysis- Plugin
- biouml.plugins.chipmunk (ChIPMunk plugin)
[edit] Description
The ChIPHorde extension can be used to discover multiple significant motifs in a given dataset using two independent filtering strategies.
[edit] Parameters:
- 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.
More about ChipHorde at: http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_v3_manual.txt
