Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Availability and Restrictions
The following versions of Trinity are available on OSC clusters:
| Version | Cardinal |
|---|---|
| 2.15.2 | X |
You can use module spider trinityrnaseq to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Access
Trinity is available to all OSC users. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
Broad Institute and the Hebrew University of Jerusalem, Open source
Usage
Usage on Cardinal
Set-up
To configure your environment for use of Trinity, run the following command:
module load trinityrnaseq/version. For example, use module load trinityrnaseq/2.15.2 to load Trinity 2.15.2.Usage
Trinity is installed in an Apptainer container. The
TRINITY_IMG environment variable contains the container image file path. If you would like to run other Trinity or other Trinity-supported analyses, you can run them by refferring to their path in the container. For example, with TrinityStats.pl:apptainer exec -e $TRINITY_IMG /usr/local/bin/util/TrinityStats.pl
For convenience, a wrapper script has been provided for the main Trinity program. It can be run as follows:
Trinity --version
For more information about Apptainer/Singularity usages, please read the OSC Apptainer/Singularity page.
Further Reading
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