The RF NormFactor module takes an arbitrary number of RC files (for example corrisponding to multiple replicates or different conditions of the same experiment) and derives transcriptome-wide (and experiment-wide) normalization factors for use with rf-norm.
For details on the different scoring and normalization methods, please refer to the RF Norm page.

Usage

$ rf-normfactor [options] -t treated.rc
$ rf-normfactor [options] -t treated.rc -u untreated.rc
$ rf-normfactor [options] -t treated.rc -u untreated.rc -d denatured.rc

To list all available parameters, simply type:

$ rf-normfactor -h

Parameter	Type	Description
-u or --untreated	string[,string]	A comma-separated list of untreated sample RC files (required by Ding/Siegfried scoring methods) Note: if a single file is passed, this will be used for all treated files
-t or --treated	string[,string]	A comma-separated list of treated sample RC files
-d or --denatured	string[,string]	A comma-separated list of denatured sample RC files (optional for Siegfried scoring methods) Note: if a single file is passed, this will be used for all treated files
-i or --index	string	RCI index file
-wl or --whitelist	string	A text file containing a list of IDs of transcripts to be used for calculating normalization factors (Default: use all transcripts)
-p or --processors	int	Number of processors (threads) to use (Default: 1)
-o or --output	string	Output file normalization factors will be reported to (Default: norm_factors.txt)
-ow or --overwrite		Overwrites the output file (if it already exists)
-sm or --scoring-method	int	Method for score calculation (1-4, Default: 1): 1. Ding et al., 2014 2. Rouskin et al., 2014 3. Siegfried et al., 2014 4. Zubradt et al., 2016
-nm or --norm-method	int	Method for signal normalization (1-3, Default: 1): 1. 2-8% Normalization 2. 90% Winsorizing 3. Box-plot Normalization
-rb or --reactive-bases	string	Reactive bases to consider for signal normalization (Default: all [ACGT]) Note: This parameter accepts any IUPAC code, or their combination (e.g. -rb M, or -rb AC)
-mc or --min-coverage	int	Discards any base with coverage below this threshold (≥1, Default: 10)
-ec or --median-coverage	float	Discards transcripts having median coverage below this threshold (≥ 0, Default: 0)
-rn or --run-norm		Automatically runs rf-norm with the derived normalization factors on the input files Note: the default output folder name of rf-norm will be used, with appended _normfactor suffix. Any pre-existing folder with the same name wil be overwritten
-rf or --rf-norm		Path to rf-norm executable (Default: assumes rf-norm is in PATH)
		Scoring method #1 options (Ding et al., 2014)
-pc or --pseudocount	float	Pseudocount added to reactivities to avoid division by 0 (>0, Default: 1)
-s or --max-score	float	Score threshold for capping raw reactivities (>0, Default: 10)
		Scoring method #3 options (Siegfried et al., 2014)
-mu or --max-untreated-mut	float	Maximum per-base mutation rate in untreated sample (≤1, Default: 0.05 [5%])
		Scoring methods #1 and #3 options (Ding et al., 2014 & Siegfried et al., 2014)
-il or --ignore-lower-than-untreated		Bases having raw reactivity in the treated sample lower than the untreated control, will be ignored (not used during reactivity normalization)
		Scoring methods #3 and #4 options (mutational profiling)
-mm or --max-mutation-rate	float	Maximum per-base mutation rate (≤1, Default: 1 [100%])