seismic-rna
About
Install
Step-By-Step
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
Commands, Arguments, Options
seismicrna package
File Formats
Data Structures
Algorithms
Bugs and Requests
How to Write this Manual
seismic-rna
How To
Run SEISMIC-RNA
Demultiplex: Split multiplexed FASTQ files by their barcodes
View page source
Demultiplex: Split multiplexed FASTQ files by their barcodes
[WRITE ME]