4.5.6 Periodicity

Function

rpf_Periodicity calculates frame-specific read distribution and 3-nt periodicity from a merged density file.

Strong 3-nt periodicity is a key Ribo-seq quality-control signal and should be checked before codon-level analysis.

Input files

Input	Description
Merged density file	Usually RIBO_merged.txt generated by rpf_Merge.
Transcript annotation	Optional normalized transcript annotation file.
Read-count threshold	Minimum read count used to retain transcripts.

Parameters

Parameter	Required	Description
-r	Yes	Input merged density file in TXT format.
-o	Yes	Output prefix.
-t	No	Input transcript annotation file in TXT format. Optional in the parser.
-m	No	Retain transcripts with more than this number of RPFs. Default is 50.
--tis	No	Number of codons after TIS to discard. Default is 0.
--tts	No	Number of codons before TTS to discard. Default is 0.

Output files

Output	Description
<prefix>_periodicity.txt	Frame-specific count and ratio table.
<prefix>_count_periodicity_plot.pdf / <prefix>_count_periodicity_plot.png	Frame-specific count plot.
<prefix>_ratio_periodicity_plot.pdf / <prefix>_ratio_periodicity_plot.png	Frame-specific ratio plot.
<prefix>.log	Running log if redirected by the user.

Example

rpf_Periodicity \
    -r ../05.merge/RIBO_merged.txt \
    -o RIBO \
    -m 50 \
    --tis 0 \
    --tts 0 \
    &> RIBO.log

Merge related results

merge_period

Merge periodicity tables from multiple samples or analyses.

Parameter	Required	Description
-l / --list	Yes	Input *_periodicity.txt files. Multiple files can be provided.
-o	Yes	Output prefix. The output table is <prefix>_periodicity.txt.

merge_period \
    -l *_periodicity.txt \
    -o RIBO

Notes

• High-quality Ribo-seq data should show strong enrichment in one reading frame.
• Low periodicity suggests that codon-level analyses should be interpreted cautiously.
• Increasing --tis or --tts can help remove boundary effects around start and stop codons.