seismic fold

Purpose

seismic fold uses per-position mutation rates to predict RNA secondary structures using one of two external folding programs. It normalizes the mutation rates into reactivity scores and passes them as soft constraints to guide the structure prediction.

Requires either RNAstructure (Fold/ShapeKnots) or ViennaRNA (RNAfold/RNAsubopt) depending on the --fold-backend setting.

Inputs

Table CSV files or table output directories: Per-position mutation rate tables produced by seismic table. Pass a table CSV, the directory containing it, or a higher-level directory. See Specify Input Files.

Outputs

All outputs go into {out}/{sample}/fold/{ref}/{reg}/.

{profile}.ct: One CT file per mutational profile, named {reg}__average.ct (or {reg}__cluster-{K}-{k}.ct for clustered data); contains the predicted base pairs. See Connectivity Table (CT): RNA secondary structures.
fold-report.json: Summary of settings and results. See Fold Report.

Quick example

Fold filter output using the default DMS settings:

seismic fold out/sample-1/filter/ref-1

Options

Backend

--fold-backend {auto|rnastructure|viennarna}: Folding program to use. auto (default): uses RNAstructure for DMS, ViennaRNA otherwise.
--pseudoknots/--no-pseudoknots: Predict pseudoknotted structures using ShapeKnots (requires RNAstructure; default off).

Reactivity normalization

--fold-quantile F: Winsorize reactivities to this quantile before folding (default 0.95).
--fold-energy-method {auto|cordero|deigan|eddy}: How to convert reactivities to folding energy penalties (default auto).
--deigan-slope F: Slope (kcal/mol) for the Deigan energy method (default 1.8).
--deigan-intercept F: Intercept (kcal/mol) for the Deigan energy method (default −0.6).

Folding conditions

--fold-temp F: Temperature in Celsius (default 37.0).
--fold-md N: Maximum base-pair distance in nucleotides; 0 for no limit (default 0).
--fold-isolated/--fold-stacked: Allow isolated (non-stacked) base pairs (default off).

Output structures

--fold-mfe/--fold-sub: Predict only the minimum-free-energy structure (default off = predict suboptimal structures as well).
--fold-max N: Maximum number of suboptimal structures to output (default 20).
--fold-percent F: Stop outputting structures when energy exceeds MFE by this % (default 20).

Constraints

--fold-constraint FILE: Force specific bases to be paired or unpaired from a constraint file.

Region selection

--fold-coords REF FIRST LAST: Fold only positions FIRST–LAST of REF.
--fold-primers REF FWD REV: Define the region by primer sequences.
--fold-regions-file FILE: Define regions to fold from a CSV file.

Branches

--branch NAME (-b): Write outputs to {out}/{sample}/fold_{NAME}/. See Branches.

Performance

--num-cpus N — multiprocessing; see Parallelize Tasks. --force — overwrite existing outputs.

The auto-generated Command Line Reference lists every option with its current default.

Common unexpected results

All structures have very few base pairs: Mutation rates may be too high or not normalized correctly. Check that the probe preset (DMS vs. SHAPE) and --fold-quantile are appropriate for your data.
Fold fails immediately: The required backend (RNAstructure or ViennaRNA) may not be installed. Check that Fold, ShapeKnots, RNAfold, or RNAsubopt is on your PATH.