Trinity

Trinity is used for de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived.

The Trinity module at CSC also includes TransDecoder and Trinotate tools to analyze the results of a Trinity run.

• Trinity
  • License
  • Available
  • Usage
    • Using Trinity
  • More information

License

Free to use and open source under Broad Institute License.

Available

Roihu-CPU: 2.15.2

Usage

Using Trinity

Trinity is set up with the command:

module load trinity

Trinity should be used interactively in a compute node or preferably through the batch job system. Below is an example batch job file for Trinity.

#!/bin/bash 
#SBATCH --job-name=trinity
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --time=48:00:00
#SBATCH --ntasks=1
#SBATCH --nodes=1  
#SBATCH --cpus-per-task=6
#SBATCH --mem=24000
#SBATCH --account=project_1234567
#SBATCH --partition=small

module load trinity/2.15.2

Trinity --seqType fq --max_memory 22G --left reads.left.fq --right \
reads.right.fq --SS_lib_type RF --CPU $SLURM_CPUS_PER_TASK \
--output trinity_run_out 

The batch script above reserves 6 computing cores from one node for the job. The maximal run time of the sample job here is 48 hours. About 4 GB of memory is reserved for each core so the total memory reservation is 6 * 4 GB = 24 GB. On Roihu, you must use batch job option --account= to define the project to be used. You should replace project_1234567 used in the example with your own project. You can check your projects with command: csc-projects.

In the actual Trinity command the number of computing cores to be used (--CPU) is set using the environment variable $SLURM_CPUS_PER_TASK. This variable contains the value set by the --cpus-per-task Slurm option.

Option --grid-exec not currently available in Roihu

The --grid-exec option is not currently available on Roihu.

When the batch job file is ready, it can be submitted to the batch queue system with the command:

sbatch batch_job_file

Look here for more information about running batch jobs.

Please also check the Trinity website to get hints for estimating the required resources.

AutoTrinotate is currently not available on Roihu. We are looking into adding it.

More information

• Trinity home page

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