Software: Subread
Description
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.
Available Versions
| Unspecified: | 1.6.4 2.0.1 |
|---|
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.
For more information, please check its website: https://biocontainers.pro/tools/subread and its home page: http://subread.sourceforge.net.
Commands
- detectionCall
- exactSNP
- featureCounts
- flattenGTF
- genRandomReads
- propmapped
- qualityScores
- removeDup
- repair
- subindel
- subjunc
- sublong
- subread-align
- subread-buildindex
- subread-fullscan
- txUnique
Module
You can load the modules by:
module load biocontainers
module load subread
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run Subread on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=subread
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers subread
featureCounts -s 2 -p -Q 10 -T 4 -a genome.gtf -o featurecounts.txt mapped.bam