RF Correlate allows calculating pairwise Pearson correlations of structure probing experiments. It can be invoked either on individual transcripts or on whole XML folders.
Overall, as well as per-transcript correlations are reported in CSV format.


To list the required parameters, simply type:

$ rf-correlate -h
Parameter Type Description
-p or --processors int Number of processors to use (Default: 1)
-o or --output string Output CSV file (Default: rf_correlate.csv)
-ow or --overwrite Overwrites output file (if the specified file already exists)
-m or --min-values float Minimum number of values to calculate correlation (Default: off)
Note: if a value between 0 and 1 is provided, this is interpreted as a fraction of the transcript's length
-s or --skip-overall Skips overall experiment correlation calculation (faster)


When --min-values specified value is interpreted as a fraction of the transcript's length, only reactive bases (specified by the XML reactive attribute; for additional details, please refer to the RF Norm documentation) are considered. For example, if a transcript containing 25% of each base has been modified with DMS (than only modifies A/C residues), setting --min-values to 0.5 will cause RF Correlate to skip the transcript if more than 50% of the A/C residues are NaNs.