Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.

StringTie is free, open source software released under an Artistic Licen

References:

• Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT & Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 2015, doi:10.1038/nbt.3122
• Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nature Protocols 11, 1650-1667 (2016), doi:10.1038/nprot.2016.095

• https://ccb.jhu.edu/software/stringtie/index.shtml

• Module Name: stringtie (see the modules page for more information)
• Multithreaded

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load stringtie
[user@cn3144 ~]$ stringtie <aligned_reads.bam> -p $SLURM_CPUS_PER_TASK [other options]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. stringtie.sh). For example:

#!/bin/bash
set -e
module load stringtie
stringtie <aligned_reads.bam> -p $SLURM_CPUS_PER_TASK [other options]

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=10g stringtie.sh

Create a swarmfile (e.g. stringtie.swarm). For example:

cd dir1; stringtie aligned_reads.bam -p $SLURM_CPUS_PER_TASK [other options]
cd dir2; stringtie aligned_reads.bam -p $SLURM_CPUS_PER_TASK [other options]
cd dir3; stringtie aligned_reads.bam -p $SLURM_CPUS_PER_TASK [other options]

Submit this job using the swarm command.

swarm -f stringtie.swarm g 10 -t 4 --module stringtie

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t #	Number of threads/CPUs required for each process (1 line in the swarm command file).
--module	Loads the module for each subjob in the swarm