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Start an interactive job, with a walltime of 12 hours, 2000MB of memory. Load related modules:

srun --pty -p interactive -t 0-12:0:0 --mem 3G -c 2 /bin/bash

Create a directory in home, download and compile trinity:

mkdir -p ~/pub/trinity
cd ~/pub/trinity
wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz
tar xvzf Trinity-v2.6.6.tar.gz 
cd trinityrnaseq-Trinity-v2.6.6/
module load gcc/6.2.0   python/2.7.12 java/jdk-1.8u112
make 
make plugins

Create a directory in home and download salmon. Note: this a binary, does not need to compile

mkdir -p ~/pub/salmon
cd ~/pub/salmon
wget https://github.com/COMBINE-lab/salmon/releases/download/v0.10.0/salmon-0.10.0_linux_x86_64.tar.gz 
tar xvzf salmon-0.10.0_linux_x86_64.tar.gz

Test run Trinity using test data

module load gcc/6.2.0 python/2.7.12 java/jdk-1.8u112 samtools/1.3.1 jellyfish/2.2.6 bowtie2/2.2.9 
export PATH=~/pub/salmon/salmon-0.10.0_linux_x86_64/bin:~/pub/trinity/trinityrnaseq-Trinity-v2.6.6:$PATH

cd ~/pub/trinity/trinityrnaseq-Trinity-v2.6.6/sample_data/test_Trinity_Assembly/
Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 2 


export TRINITY_HOME=~/pub/trinity/trinityrnaseq-Trinity-v2.6.6
module load blat/35
$TRINITY_HOME/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --query trinity_out_dir/Trinity.fasta \
	--target __indiv_ex_sample_derived/refSeqs.fa --no_reuse

For downstream analysis, please visit: https://github.com/trinityrnaseq/trinityrnaseq/wiki

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