Run SEISMIC-RNA
You can run the SEISMIC-RNA workflow in two ways:
Run all steps automatically using
seismic wf(see Workflow: Run all steps).Run each step individually using its command (e.g.
seismic alignfor the Align step).
- 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