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
genRandomReads
propmapped
qualityScores
removeDup
repair
subindel
subjunc
sublong
subread-align
subread-buildindex
subread-fullscan
txUnique
Example job
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run subread on our clusters:
#!/bin/bash
#SBATCH -p PartitionName # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=subread
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module purge
module load subread/XXXX ### you can run *module avail subread* to check all available versions
featureCounts -s 2 -p -Q 10 -T 4 -a genome.gtf -o featurecounts.txt mapped.bam