Difference between revisions of "ChIP-seq Quality control analysis"

Latest revision as of 18:14, 9 December 2020

Analysis title

ChIP-seq Quality control analysis

Provider

Institute of Systems Biology

Class

ChIPseqQCAnalysis

Plugin

biouml.plugins.gtrd (GTRD)

[edit] Description

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

[edit] 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