seismic importmm

Purpose

seismic importmm converts RNA Framework Mutation Map (MM) files into the IDmut batch format used by SEISMIC-RNA. Use it if you generated mutation data with RNA Framework or DRACO and want to continue analysis (filter, cluster, fold, etc.) in SEISMIC-RNA without re-aligning.

Inputs

Mutation Map (MM) files: One or more .mm files from RNA Framework or DRACO. See Specify Input Files.

Outputs

All outputs go into {out}/{sample}/idmut/{ref}/, mirroring the output of seismic idmut.

idmut-batch-{num}.brickle: Per-read, per-position mutation calls.
idmut-report.json: Summary of settings and results.

Quick example

Import MM files for a sample named my-sample:

seismic importmm --sample my-sample data/*.mm

Options

Required

--sample NAME (-s): Name to give the imported sample.

Quality filters

--min-reads N (-N): Skip MM files with fewer than N reads (default 1000).
--batch-size N: Maximum reads per output batch (default 65536).

Branches

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