4.7.3 Codon decoding time

Function

rpf_CDT estimates codon decoding time by combining matched Ribo-seq and RNA-seq density tables. It normalizes codon-level RPF signal by RNA-seq signal and reports codon-level decoding-time summaries and plots.

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 annotation table	Normalized gene annotation table, for example gene.norm.txt.

Parameters

Parameter	Required	Description
--rpf	Yes	Input RPF density table in TXT format.
--rna	Yes	Input RNA-seq density table in TXT format.
-l	Yes	Gene annotation or gene list file in TXT format.
-o	Yes	Output prefix.
-s	No	Ribosomal site used for CDT calculation. Choices: E, P, A. Default: P.
-f	No	Reading frame used for CDT calculation. Choices: 0, 1, 2, all. Default: all.
-m	No	Retain transcripts with more than this minimum number of RPFs. Default: 30.
--tis	No	Number of codons after the translation initiation site to discard. Default: 15.
--tts	No	Number of codons before the translation termination site to discard. Default: 5.
--scale	No	Scaling method for relative CDT 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>_cdt.txt	Codon decoding time summary table.
<prefix>_cdt_corr.txt	Correlation matrix calculated from normalized CDT values.
<prefix>_cdt_corrplot.pdf / .png	CDT correlation heatmap.
<prefix>_cdt_heatplot.pdf / .png	CDT heatmap.

Example

for site in E P A
do
    rpf_CDT \
        -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

• CDT requires matched Ribo-seq and RNA-seq density tables. Gene names must be consistent between the two files.
• The command uses the gene annotation file to define transcript structure and transcript length information.
• CDT is useful for comparing codon-level elongation-related patterns across samples or conditions.

Merge related results

Use merge_cdt to merge multiple CDT result tables:

merge_cdt -l *_cdt.txt -o RIBO