Analysis Reports¶
The FlowAgent analysis report functionality provides comprehensive insights into your workflow outputs. It analyzes quality metrics, alignment statistics, and expression data to generate actionable recommendations.
Running Analysis Reports¶
# Basic analysis
flowagent "analyze workflow results" --analysis-dir=/path/to/workflow/output
# Focus on specific aspects
flowagent "analyze quality metrics" --analysis-dir=/path/to/workflow/output
flowagent "analyze alignment rates" --analysis-dir=/path/to/workflow/output
flowagent "analyze expression data" --analysis-dir=/path/to/workflow/output
The analyzer will recursively search for relevant files in your analysis directory, including: - FastQC outputs - MultiQC reports - Kallisto results - Log files
Report Components¶
Summary¶
- Number of files analyzed
- QC metrics processed
- Issues found
- Recommendations
Quality Control Analysis¶
- FastQC metrics and potential issues
- Read quality distribution
- Adapter contamination levels
- Sequence duplication rates
Alignment Analysis¶
- Overall alignment rates
- Unique vs multi-mapped reads
- Read distribution statistics
Expression Analysis¶
- Gene expression levels
- TPM distributions
- Sample correlations
Recommendations¶
- Quality improvement suggestions
- Parameter optimization tips
- Technical issue resolutions
Report Output¶
By default, the analysis report is:
- Displayed in the console
- Saved as a markdown file (analysis_report.md) in your analysis directory
To only view the report without saving:
flowagent "analyze workflow results" --analysis-dir=results --no-save-report