4.7.6 Meta-codon analysis

Function

rpf_Meta_Codon extracts average RPF density around selected codons or codon motifs. It can process single codons such as AAA or multi-codon motifs whose length is a multiple of three.

Input files

Input	Description
RPF density table	Merged Ribo-seq density table, usually RIBO_merged.txt.
Codon list	Optional one-column TXT file containing codons or codon motifs. If omitted, all codons from the codon table are used.
Gene list	Optional transcript or gene list. If not provided, all genes are used.

Parameters

Parameter	Required	Description
-r	Yes	Input RPF density table in TXT format.
-l	No	Gene name or transcript ID list in TXT format. If omitted, all genes are used.
-c	No	One-column codon or codon-motif list in TXT format. RNA U is converted to DNA T. If omitted, all codons are used.
-o	Yes	Output prefix.
-f	No	Reading frame used for meta-codon analysis. Choices in the parser are 0, 1, 2; the script default is all.
-a	No	Number of upstream and downstream codons to retrieve around each target codon or motif. Default: 20.
-m	No	Retain transcripts with more than this minimum number of RPFs. Default: 50.
--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.
-n	No	Normalize RPF counts to RPM before extracting meta-codon profiles. Disabled by default.
-u	No	Remove overlapping repeated target codons within the same window to reduce background noise. Disabled by default.
-s	No	Scale window density by gene-level density. Disabled by default.
--smooth	No	Smooth density values using a Savitzky-Golay filter. Format: window,order, for example 3,1. Disabled by default.
--thread	No	Number of threads. Default: 1. The current implementation loops over codons sequentially.
--fig	No	Draw meta-codon line plots. Disabled by default.

Output files

Output	Description
<prefix>_<codon>_<site_num>_<valid_site_num>_meta_density.txt	Meta-density table around the selected codon or codon motif.
<prefix>_<codon>_<site_num>_<valid_site_num>_meta_sequence.txt	Sequence context table for the selected codon or codon motif.
<prefix>_<codon>.pdf / .png	Meta-codon line plot. Generated only with --fig.

Codon list example

AAA
AAG
ATG
GCTGAA

Example

rpf_Meta_Codon \
    -r ../05.merge/RIBO_merged.txt \
    -m 50 \
    -f 0 \
    -c codon_list.txt \
    -a 15 \
    -u \
    -n \
    --fig \
    -o RIBO \
    &> RIBO_meta_codon.log

Notes

• The command imports A-site density internally from the merged RPF table.
• Target motifs must have lengths divisible by three; otherwise they are skipped.
• The output file name records both the total number of matched sites and the number of valid sites after optional filtering.
• Use -u when repeated target codons within the same window may inflate local background signal.