RF Combine allows combining XML files from multiple experiments into a single profile.
For example, this can be useful when performing CIRS-seq experiments, to combine into a single profile both the reactivity of A/C residues probed with DMS, and of G/U residues probed with CMCT.
Alternatively, RF Combine is able to combine into a single profile multiple replicates of the same probing experiment. In these cases, the resulting XML files may contain optional “-error” tags, in which the per-base standard deviation of the measure from each experiment is reported.
When combining datasets containing NaN values, only non-NaN positions in all experiments will be combined, while the others will be reported as NaNs as well.
There is no limit to the number of experiments that RF Combine can handle. It can be used both on individual XML files, or on whole XML folders generated by either RF Norm, RF Silico, or RF ModCall.


RF Combine does not allow combining RF Norm XML files generated using different scoring/normalization methods, since this will produce inconsistent data.


In XML files generated using RF Combine, the combined attribute of the transcript tag is set to TRUE.


To list the required parameters, simply type:

$ rf-combine -h
Parameter Type Description
-p or --processors int Number of processors (threads) to use (Default: 1)
-o or --output-dir string Output directory for writing combined data in XML format (Default: combined/)
-ow or --overwrite Overwrites the output directory if already exists
-s or --stdev When combining multiple replicates, an optional "-error" tag will be reported in the output XML files, containing the per-base standard deviation of the measure
-d or --decimals int Number of decimals for reporting reactivities (1-10, Default: 3)