Difference between revisions of "ChIPHorde (analysis)"
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==== Description ==== | ==== Description ==== | ||
| + | The ChIPHorde extension can be used to discover multiple significant motifs in a given dataset using two independent filtering strategies. | ||
| + | |||
| + | ==== 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 http://autosome.ru/smbsm/librettos/libretto_chipmunk/chipmunk_v3_manual.txt] | ||
| + | |||
[[Category:Analyses]] | [[Category:Analyses]] | ||
[[Category:ChIPMunk (analyses group)]] | [[Category:ChIPMunk (analyses group)]] | ||
[[Category:Autosome.Ru analyses]] | [[Category:Autosome.Ru analyses]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Revision as of 13:17, 27 June 2013
- Analysis title
ChIPHorde
- Provider
- Autosome.Ru
- Class
ChipHordeAnalysis- Plugin
- biouml.plugins.chipmunk (ChIPMunk plugin)
Description
The ChIPHorde extension can be used to discover multiple significant motifs in a given dataset using two independent filtering strategies.
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
