The RF JackKnife takes one or more XML reactivity files, and a set of reference RNA structures in dotbracket notation, and iteratively calls rf-fold by tuning the slope and intercept folding parameters. This is useful to calibrate the folding parameters for a specific probing reagent or experiment type.
It produces 3 CSV tables respectively containing the positive predictive value (PPV), sensitivity, and the geometric mean of the 2 values for each slope/intercept pair.

PPV Sensitivity table

Usage

To list the required parameters, simply type:

$ rf-jackknife -h
Parameter Type Description
-r or --reference string A file containing reference structures in Vienna format (dotbracket notation)
-p or --processors int Number of processors to use (Default: 1)
-o or --output-dir string Output directory (Default: rf_jackknife/)
-t or --tmp-dir string Temporary directory (Default: /tmp)
-ow or --overwrite Overwrites output directory (if the specified path already exists)
-sl or --slope float,float Range of slope values to test (Default: 0,5)
-in or --intercept float,float Range of intercept values to test (Default: -3,0)
-ss or --slope-step float Step for testing slope values (Default: 0.2)
-is or --intercept-step float Step for testing intercept values (Default: 0.2)
-x or --relaxed Uses relaxed criteria (described in Deigan et al., 2009) to calculate PPV and sensitivity
-kn or --keep-noncanonical Keeps non-canonical basepairs in reference structure
-kp or --keep-pseudoknots Keeps pseudoknotted basepairs in reference structure
-kl or --keep-lonelypairs Keeps lonely basepairs (helices of length 1 bp) in reference structure
-m or --median Reports the median PPV/sensitivity value between all reference structures
Note: by default, the geometric mean of PPV/sensitivity values is reported
-am or --arithmetic-mean Reports the arithmetic mean of PPV/sensitivity values between all reference structures
Note: by default, the geometric mean of PPV/sensitivity values is reported
-rf or --rf-fold string Path to rf-fold executable (Default: assumes rf-fold is in PATH)
-rp or --rf-fold-params string Manually specify additional RF Fold parameters (e.g. -rp "-md 500 -m 2")


Output CSV files

RF PeakCall produces 3 CSV files, one for PPV, one for sensitivity, and one with the geometric mean of the 2 values, with intercept values on the x-axis, and slope values on the y-axis