Subread

Subread is a collection of tools for processing sequencing reads.

Availability

Cluster	Module/Version
BOSE	subread/2.1.1
BGSC	N/A

Note: You can simply use module load subread to activate the most recently installed version of this software.

Commands / Arguments

This is a list of some included commands in the Subread suite that we wanted to highlight. Use the official guide for a full list of included tools, arguments, and options.

Option	Description
subread-align	The main Subread aligning tool
subjunc	RNA-sequence aligner for detecting exon-exon junctions
featureCounts	General-purpose read summarization

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load subread                                         # Load Subread
/data/software/default/subread/2.1.1/test/test_all.sh       # Run the built-in test script to ensure Subread is functioning

Real Example

Has your research group used Subread in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation(s) in your papers to support continued development of Subread and its included tools. Please use the citation(s) appropriate for the individual tool(s) used in authoring your papers.

If you use featureCounts, you can cite:

Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30. http://www.ncbi.nlm.nih.gov/pubmed/24227677

If you use Subread or Subjunc aligners, you can cite:

Liao Y, Smyth GK and Shi W (2013). The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108. http://www.ncbi.nlm.nih.gov/pubmed/23558742

If you use Rsubread, you can cite:

Liao Y, Smyth GK and Shi W (2019). The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Research, 47(8):e47. http://www.ncbi.nlm.nih.gov/pubmed/30783653

If you use cellCounts, you can cite:

Liao Y, Raghu D, Pal B, Mielke LA and Shi W (2023). cellCounts: an R function for quantifying 10x Chromium single-cell RNA sequencing data. Bioinformatics, 39(7):btad439. http://www.ncbi.nlm.nih.gov/pubmed/37462540

If you use Rsubread inbuilt annotations, you can cite:

Chisanga D, Liao Y and Shi W (2022). Impact of gene annotation choice on the quantification of RNA-seq data. BMC Bioinformatics, 23(1):107. http://www.ncbi.nlm.nih.gov/pubmed/35354358