Sites Motifs Analysis

Analysis title

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