4.7.4 Codon selection time

Function

rpf_CST estimates codon selection time using matched Ribo-seq and RNA-seq density tables. It iteratively calculates codon-level selection-time values and outputs both detailed iterative results and final codon-level summaries.

Input files

Input	Description
RPF density table	Merged Ribo-seq density table, usually RIBO_merged.txt.
RNA density table	Merged RNA-seq density table, usually RNA_merged.txt.
Gene list	Optional transcript or gene list. If not provided, all genes shared by the two density tables are used.

Parameters

Parameter	Required	Description
--rpf	Yes	Input RPF density table in TXT format.
--rna	Yes	Input RNA-seq density table in TXT format.
-l	No	Gene name or transcript ID list in TXT format. If omitted, all genes are used.
-o	Yes	Output prefix.
-s	No	Ribosomal site used for CST calculation. Choices: E, P, A. Default: P.
-f	No	Reading frame used for CST calculation. Choices: 0, 1, 2, all. Default: all.
-m	No	Retain transcripts with more than this minimum number of RPFs. Default: 30.
-t	No	Number of iterations used for CST calculation. Default: 10.
--tis	No	Number of codons after the translation initiation site to discard. Default: 0.
--tts	No	Number of codons before the translation termination site to discard. Default: 0.
--scale	No	Scaling method for relative CST values. Choices: zscore, minmax. Default: minmax.
--stop	No	Remove stop codons from codon-level summary tables and heatmaps. Disabled by default.

Output files

Output	Description
<prefix>_iterative_codon_selection_time.txt	Detailed CST values for each iteration and sample.
<prefix>_codon_selection_time.txt	Final codon-level CST table containing absolute and relative CST values.
<prefix>_cst_corr.txt	Correlation matrix calculated from absolute CST values.
<prefix>_cst_corrplot.pdf / .png	CST correlation heatmap.
<prefix>_cst_heatplot.pdf / .png	CST heatmap.

Example

for site in E P A
do
    rpf_CST \
        -l ../../../1.reference/norm/gene.norm.txt \
        --rna ../../../3.rna-seq/5.riboparser/05.merge/RNA_merged.txt \
        --rpf ../05.merge/RIBO_merged.txt \
        --stop \
        -m 50 \
        -f 0 \
        -s ${site} \
        --tis 10 \
        --tts 5 \
        -o ${site}_site \
        &> ${site}_site.log
done

Notes

• CST requires matched Ribo-seq and RNA-seq density tables. Gene names must be consistent between the two files.
• Increase -t when more iterative refinement is needed, but this also increases runtime.
• CST and CDT are related but not identical. CDT reports a direct decoding-time estimate, while CST performs iterative codon selection-time estimation.

Merge related results

Use merge_cst to merge multiple CST result tables:

merge_cst -l *_codon_selection_time.txt -o RIBO