Sites Motifs Analysis

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Analysis title
Default-analysis-icon.png Sites Motifs Analysis
Provider
Institute of Systems Biology
Class
SitesMotifsAnalysis
Plugin
biouml.plugins.gtrd (GTRD)

Description

Count motives for SQL track + HOCOMOCO track

Parameters:

  • Sequences collection – Select a source of nucleotide sequences
    • Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
    • Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
  • Site name – Name of predicted sites
  • Path to track – Path to track with ChIP-Seq dataset
  • Use HOCOMOCO track – Choose HOCOMOCO track or use HOCOMOCO model for creating new HOCOMOCO track
  • output table name – write output table name
  • Record result to GTRD database – Record result to GTRD database
  • write new table – record new table to GTRD database
  • write data to existed table – record data to existed table in GTRD database
  • nameOfExistedTable – nameOfExistedTable
  • Number of thread – write number of threads (not more than 20)
  • onlyTrackl – onlyTrackl
  • Use only one model – Use only one HOCOMOCO model
  • Count cover of motifs – choose this one, if you need to count cover of motifs in sites
  • Use mouse matrix – Use mouse HOCOMOCO matrix
  • miniml site size – Choose miniml site's size
  • model name – write name of your model
  • Track's names in folder – Track's names in folder
  • modelPath – modelPath
  • Path to output folder – Path to output folder
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