4 Workflow overview¶
The workflow is organized as a complete tutorial. Each step contains detailed commands, parameter explanations, and expected outputs.
Main workflow¶
The first four steps belong to the public pipeline and can be handled by general bioinformatics tools (e.g. STAR, Bowtie, RSEM). The remaining steps are the RiboParser-specific analysis.
# 4.1-4.4: Public pipeline (general tools)
Reference preparation
→ Raw data download
→ Raw data cleaning
→ Alignment and quantification
# 4.5-4.9: RiboParser-specific analysis
→ Quality control
→ Gene-level analysis
→ Codon-level analysis
→ smORF analysis
→ SeRP analysis
| Step | Page | Purpose |
|---|---|---|
| 4.1 | Reference preparation | Build genome, transcriptome, Bowtie, STAR, RSEM, and normalized RiboParser references |
| 4.2 | Raw data download | Download public or user-provided RNA-seq/Ribo-seq data |
| 4.3 | Raw data cleaning | Trim adapters and filter reads |
| 4.4 | Alignment and quantification | Classify reads, align to genome, and quantify expression (RNA-seq and Ribo-seq pipelines) |
| 4.5 | Quality control | Check library quality and generate density matrices |
| 4.6 | Gene-level analysis | Quantification, coverage, correlation, and density retrieval |
| 4.7 | Codon-level analysis | Pausing, occupancy, decoding time, selection time, CoV, meta-codon, and odds ratio |
| 4.8 | smORF analysis | Scan, cluster, evaluate, and quantify smORF candidates |
| 4.9 | SeRP analysis | Peak, overlap, and property analysis |
Notes¶
- Steps 4.1-4.4 are shared with any standard RNA-seq/Ribo-seq project and can be handled by other general tools.
- Steps 4.5-4.9 are RiboParser-specific and should be run in order, because later modules consume the reference files, merged density matrices, and normalized annotations produced by earlier steps.