4.6 Gene-level analysis

Function

Gene-level analysis summarizes Ribo-seq or RNA-seq density at transcript and gene scale. These modules quantify CDS-level abundance, evaluate metagene coverage, estimate gene-body coverage percentage, measure sample correlation, and retrieve selected gene density profiles for downstream visualization.

Submodules

Section	Command	Description
4.6.1 Gene quantification	rpf_Quant	Summarize RPF counts, RPM, RPKM, and TPM for CDS and optional UTR regions.
4.6.2 Gene coverage	rpf_Coverage, rpf_Percent	Generate metagene coverage profiles and calculate per-gene coverage percentages.
4.6.3 Gene correlation	rpf_Corr	Calculate gene-level and nucleotide/RPF-level sample correlations.
4.6.4 Gene density retrieval	rpf_Retrieve	Retrieve and optionally reformat density records for selected genes or transcripts.

Recommended order

1. Run rpf_Quant after density merging to obtain gene-level abundance matrices.
2. Run rpf_Coverage and rpf_Percent to inspect whether RPF or RNA density is evenly distributed across transcripts.
3. Run rpf_Corr to evaluate reproducibility among biological replicates or sample groups.
4. Run rpf_Retrieve when selected genes need to be inspected manually or plotted with custom scripts.

Input relationship

Most commands in this section use the merged density table generated by rpf_Merge, usually named RIBO_merged.txt or RNA_merged.txt. Commands that need transcript structure, such as rpf_Coverage and rpf_Percent, also require the normalized transcript annotation file, usually gene.norm.txt.

Notes

• For standard translation-level quantification, use CDS density and trim codons near the start and stop codons to reduce initiation and termination artifacts.
• Gene-level metrics are useful for expression overview, replicate quality control, and downstream differential analysis, but they should be interpreted together with read periodicity, metagene profiles, and coverage uniformity.