SnakeMapper

This Snakemake pipeline orchestrates the Weeks and Mustoe labs' "Mapper suite" of software for RNA structure probing, modeling, and visualization.

• SHAPE-MaP reactivity profiling
• RING-MaP and PAIR-MaP correlation analysis
• DANCE-MaP deconvolution of alternative structures
• RNAstructure (Mathews Lab) folding/pairing-probability calculations
• RNAvigate figure generation

Given raw modified/untreated fastq reads and a target fasta, it runs the full suite for each sample/target pair and produces structure models, pairing probabilities, and arc plots.

Status

This pipeline is under active development. Some steps (e.g. clustered folding) are optional and can be disabled per run. See TODO.md for planned changes.

Requirements

• Snakemake (with --use-conda support)
• conda or mamba
• The following tools, installed separately and pointed to in config/config.yaml's exe_locations (see Dependencies):
  • Shapemapper2
  • RingMapper / PairMapper
  • DanceMapper
  • RNAstructure (Fold-smp, partition-smp, ProbabilityPlot)

All other Python dependencies (including RNAvigate) are installed automatically by Snakemake into per-rule conda environments via --use-conda.

Usage

1. Copy the contents of this repository into your run directory.

2. Edit config/config.yaml:

   • Set exe_locations to the paths of the tools listed above (or leave as the bare command if they're already on your $PATH).
   • Add an entry under samples for each sample/target pair, following the naming rules documented in the comments in config/config.yaml.
   • Enable/disable pipeline steps and adjust parameters as needed.

3. Run with Snakemake, e.g.:

   snakemake --use-conda --cores 8

   map_suite.sbatch is an example Slurm submission script for running on an HPC cluster; adjust the resource requests and slurm_account for your environment. To run this on a cluster that uses Slurm:

   sbatch map_suite.sbatch

There is currently no nicely bundled example dataset to run out of the box. Supply your own fastq/fasta inputs per the config format above.

Dependencies

SnakeMapper is orchestration code: it does not reimplement the underlying structure-probing analyses. If you use this pipeline, please also cite the tools it wraps:

• Shapemapper2
• RingMapper and PairMapper
• DanceMapper
• RNAstructure
• RNAvigate

License

Released under the MIT License.