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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.