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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.
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| − | ==== Parameters: ====
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| − | * '''Input sequences''' – Collection containing input reads.
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| − | * '''Start length''' – Start length of the matrix
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| − | * '''Stop length''' – Stop length of the matrix
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| − | * '''Motifs count limit''' – Maximum number of motifs to discover
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| − | * '''Filtering mode''' – Whether to mask polyN ("Mask") or to drop entire sequence ("Filter")
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| − | * '''Number of threads''' (expert) – Number of concurrent threads when processing
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| − | * '''Step limit''' (expert) – Step limit
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| − | * '''Try limit''' (expert) – Try limit
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| − | * '''GC percent''' (expert) – Fraction of GC nucleotides (0..1), set to -1 for auto
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| − | * '''ZOOPS factor''' (expert) – Zero-or-one-occurence-per-sequence factor
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| − | * '''Motif shape''' (expert) – Motif shape
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| − | * '''Use peak profiles''' (expert) – Whether to use peak profiles (if available)
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| − | * '''Output matrix library''' – Path to the matrix library to put matrix into (will be created if not specified)
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| − | * '''Matrix name prefix''' – Prefix for the matrix name. It will be followed by number.
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| − | 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]
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| | [[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]] |
ChIPHorde
