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
To list the required 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 |
-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) |
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%]) |