Tool Description
rf-index Automatically queries UCSC genome database and builds the transcriptome Bowtie reference index for the RF Count module
rf-count Performs reads pre-processing and mapping (where needed), and calculates per-base RT-stops/mutations and coverage
rf-norm Performs whole-transcriptome normalization of structure probing data
rf-fold Produces secondary structures for the analyzed transcripts using structure probing data to guide folding
rf-compare Compares secondary structures inferred by rf-fold with a set of reference structures, and computes PPV and sensitivity
rf-jackknife Iteratively optimize slope and intercept parameters to maximize PPV and sensitivity using a set of reference structures
rf-modcall Performs analysis of Ψ-seq/Pseudo-seq and 2OMe-seq data
rf-peakcall Performs peak calling of RNA immunoprecipitation (IP) experiments
rf-combine Combines results of multiple experiments into a single profile
rf-wiggle Produces WIGGLE track files from RC or XML input files

RNAFramework pipeline