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

Revision as of 16:33, 12 March 2019

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

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