rpf_Shift¶

rpf_Shift screens transcripts for frame-shift-like RPF periodicity patterns and summarizes the number of transcripts assigned to each reading frame.

Function¶

Use this command to calculate transcript-level 3-nt frame periodicity from a merged RPF density table, classify transcripts by dominant frame, and draw summary plots for frame-shift screening.

Input¶

The input should be a merged RPF density table generated by RiboParser, usually from rpf_Merge. The optional transcript list should contain one transcript/gene ID per line.

Parameters¶

Parameter	Required	Meaning
`-r`	yes	Input merged RPF density file in TXT/TSV format.
`-o`	yes	Output prefix.
`-t`	no	Transcript/gene ID list file used to restrict the analysis.
`-p`	no	Minimum dominant-frame percentage used for frame classification. Default: `45`. Although the help text mentions a range of `[0 - 1]`, the implementation calculates percentages, so values such as `45` mean 45%.
`-m`	no	Minimum total RPF count used to retain transcripts. Default: `50`.
`--tis`	no	Number of codons after the translation initiation site to discard before periodicity calculation. Default: `0`.
`--tts`	no	Number of codons before the translation termination site to discard before periodicity calculation. Default: `0`.

Output¶

The command writes transcript-level periodicity tables, per-sample frame classification files, a merged frame-count table, and summary plots:

<prefix>_gene_periodicity.txt
<prefix>_<sample>_gene_frame_shift.txt
<prefix>_gene_frame_shift_count.txt
<prefix>_gene_frame_shift_count_plot.pdf
<prefix>_gene_frame_shift_count_plot.png

The per-sample frame classification table contains each transcript's frame assignment, such as frame0, frame1, frame2, or fuzzy.

Examples¶

Run frame-shift screening with default filters:

rpf_Shift \
  -r RIBO_merged.txt \
  -o RIBO.shift

Use a transcript list and discard codons near TIS/TTS:

rpf_Shift \
  -r RIBO_merged.txt \
  -t gene.norm.txt \
  -m 50 \
  -p 45 \
  --tis 5 \
  --tts 5 \
  -o RIBO.shift

Use a stricter dominant-frame threshold:

rpf_Shift \
  -r RIBO_merged.txt \
  -t gene.norm.txt \
  -m 100 \
  -p 60 \
  -o RIBO.shift.strict

Notes¶

-p should be interpreted as a percentage threshold in the current implementation.
Transcripts whose dominant frame does not exceed the threshold are classified as fuzzy.
Use --tis and --tts to remove codons close to start/stop sites when local initiation or termination peaks distort the frame signal.
This command is a screening utility. Candidate frame-shift events should be inspected with gene-level density plots and biological annotation before final interpretation.