How To
- Run SEISMIC-RNA
- Demultiplex: Split multiplexed FASTQ files by their barcodes
- Align: Trim FASTQ files and align them to reference sequences
- Relate: Compute relationships between references and aligned reads
- Pool: Merge samples (vertically) from the Relate step
- Mask: Define mutations and sections to filter reads and positions
- Cluster: Infer alternative structures by clustering reads’ mutations
- Join: Merge sections (horizontally) from the Mask or Cluster step
- Table: Count mutations for each read and position
- Fold: Predict RNA secondary structures using mutation rates
- Graph: Plot data from tables and/or structures and compare samples
- Export: Export a file of each sample for the seismic-graph web app
- Workflow: Run all steps
- Graph Results
- List Positions Matching Criteria
- Add/Delete Orders to/from an Already-Clustered Dataset
- Clean FASTA Files
- List Input Files
- Define Sections
- Normalize Mutation Rates
- Parallelize Tasks
- Log Messages