Subread

Introduction

Subread carries out high-performance read alignment, quantification and mutation discovery. It is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and DNA-seq reads. It uses a new mapping paradigm called seed-and-vote to achieve fast, accurate and scalable read mapping. Subread automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports INDEL detection and can map reads with both fixed and variable lengths.

Versions

• 1.6.4

• 2.0.1

Commands

• detectionCall

• exactSNP

• featureCounts

• flattenGTF

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=subread     # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load subread/XXXX       ### Latest version is recommended.