ChIP-seq Quality control analysis

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Analysis title
Default-analysis-icon.png ChIP-seq Quality control analysis
Provider
Institute of Systems Biology
Class
ChIPseqQCAnalysis
Plugin
biouml.plugins.gtrd (GTRD)

Description

Processing raw Chip-seq data and calculation of quality control metrics for assessing tracks from GTRD and AUCs-applications

Parameters:

  • Data Type – Select data Type
  • ChIP-seq raw data processing parameters – ChIP-seq raw data processing parameters
    • Experiment library layout – Experiment library layout
    • FASTQ-file – ChIP-seq raw data
    • Has Input Control? – Has Input Control?
    • Input control library layout – Input control library layout
    • Reference Genome – Reference Genome
  • Select BED-files – Select BED-files
  • FPCM and FNCM Estimation Parameters – FPCM and FNCM Estimation Parameters
    • Minimal length of binding region – Binding regions shorter than the minimal length would be extended
    • Maximal length of binding region – Binding regions longer than the minimal length would be narrowed
    • FPCM threshold – If the FPCM exceeds the threshold FNCM will be calculated based on Chapman’s estimate
    • Calculate AUC? – Calculate AUC?
    • AUC Calculation Parameters – AUC Calculation Parameters
      • Path to folder with site models – Select a folder with transcription factor binding sites (TFBSs) models
      • Site model name – Select a TFBS model name
      • 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
  • Path to output folder – Path to output folder
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