Trinity¶
Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms, transcripts from recently duplicated genes and transcriptomes from Illumina RNA-seq data.
Trinity is available as a module on Apocrita.
Usage¶
To run the default installed version of Trinity, simply load the trinity
module:
module load trinity
For usage documentation, run Trinity -h.
Example job¶
Serial job¶
Here is an example job running on 2 cores and 10GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=5G
module load trinity
Trinity --seqType fq \
--max_memory 10G \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--CPU ${NSLOTS}