Trinity is a program for the efficient and robust de novo (no reference genome required) reconstruction of transcriptomes from RNA-seq data.
Trinity produces a large number of intermediate files (500,000 to 1,000,000). The MSI filesystem limits each group to a maximum of 1 million files. Therefore it is recommended that you configure Trinity to write output to /scratch (using the option "--output /scratch/trinity"), where there is no file number limit, and copy the fasta assembly file back to your group folder when Trinity has finished.
To run this software interactively in a Linux environment run the commands:
module load trinityrnaseq Trinity.pl
Several versions of Trinity are available, but the versions may be different on different platforms.To list all versions of Trinity available on the machine, type
module avail trinityrnaseq
More specific and extensive information can be found at the project homepage: http://trinityrnaseq.sourceforge.net/