4.7.5 Coefficient of Variation¶

Function¶

The coefficient-of-variation modules evaluate variability in RPF density across CDS regions. RiboParser provides two related commands:

rpf_CoV calculates gene-level CoV values from CDS RPF density and can compare CoV distributions between sample groups.
rpf_Cumulative_CoV calculates cumulative CoV along CDS positions and can output a meta table for positional visualization.

The model described for coverage-dependent CoV is:

log2(CV) = 1/2 * log2(beta / mu + alpha)

where CV is the coefficient of variation, mu is the mean coverage, and alpha / beta are fitting parameters.

4.7.5.1 rpf_CoV¶

Input files¶

Input	Description
RPF density table	Merged Ribo-seq density table, usually `RIBO_merged.txt`.
Group design file	Optional two-column sample group file. Required only for group comparison.
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.
`-g`	No	Sample group design file. If provided, group-level CoV comparison is performed.
`-l`	No	Gene name or transcript ID list in TXT format. If omitted, all genes are used.
`-o`	Yes	Output prefix. The main output is `<prefix>_CoV.txt`.
`-f`	No	Reading frame used for CoV calculation. Choices: `0`, `1`, `2`, `all`. Default: `all`.
`-m`	No	Retain transcripts with more than this minimum number of RPFs. Default: `5`.
`-n`	No	Normalize RPF counts to RPM before CoV calculation. Disabled by default.
`--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`.
`--fig`	No	Draw CoV fitting plots. Disabled by default.

Group design file¶

The group design file should contain at least two columns: Name and Group.

Name    Group
WT_ribo_YPD1    WT_ribo_YPD
WT_ribo_YPD2    WT_ribo_YPD
WT_ribo_YPD3    WT_ribo_YPD
ncs2d_ribo_YPD1 ncs2d_ribo_YPD
ncs2d_ribo_YPD2 ncs2d_ribo_YPD
ncs2d_ribo_YPD3 ncs2d_ribo_YPD

Output files¶

Output	Description
`<prefix>_CoV.txt`	Gene-level RPF sum, mean, and CoV table.
`<prefix>_compared_CoV.txt`	Group comparison statistics. Generated only when `-g` is provided.
`<prefix>_<group1>_vs_<group2>_CoV_fitplot.pdf` / `.png`	CoV fitting plot for each group comparison.

Example¶

rpf_CoV \
    -l ../../../1.reference/norm/gene.norm.txt \
    -r ../05.merge/RIBO_merged.txt \
    -f 0 \
    -m 30 \
    --tis 10 \
    --tts 5 \
    --fig \
    -g design.txt \
    -o RIBO \
    &> RIBO_CoV.log

4.7.5.2 rpf_Cumulative_CoV¶

Input files¶

Input	Description
RPF density table	Merged Ribo-seq density table, usually `RIBO_merged.txt`.
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.
`-o`	No	Output prefix. If omitted, the command uses the input file name-derived prefix.
`-l`	No	Gene name or transcript ID list in TXT format. If omitted, all genes are used.
`-m`	No	Retain transcripts with more than this minimum number of RPFs. Default: `0`.
`-n`	No	Normalize RPF counts to RPM before cumulative CoV calculation. Disabled by default.
`-t`	No	Trim transcripts to this nucleotide length for the meta cumulative CoV table. Default: `50`.
`-s`	No	Split gene-level cumulative CoV results into one file per gene. Disabled by default.
`-z`	No	Reset each CDS start position to zero-based or CDS-start-relative coordinates before output. Disabled by default.

Output files¶

Output	Description
`<prefix>_cumulative_CoV.txt`	Cumulative CoV table for all retained genes.
`<gene>_cumulative_CoV.txt`	Per-gene cumulative CoV table. Generated only with `-s`.
`<prefix>_meta<trim>_cumulative_CoV.txt`	Meta cumulative CoV table for the first `trim` nucleotides.

Example¶

rpf_Cumulative_CoV \
    -l ../../../1.reference/norm/gene.norm.txt \
    -r ../05.merge/RIBO_merged.txt \
    -m 50 \
    -n \
    -z \
    -t 300 \
    -o RIBO \
    &> RIBO_cumulative_CoV.log

Notes¶

Low-coverage transcripts often show inflated CoV. Choose -m carefully according to the sequencing depth.
The rpf_CoV command uses P-site density internally for CoV calculation.
rpf_Cumulative_CoV imports all frames from the P-site density and then reshapes the density table into nucleotide-level cumulative CoV profiles.