Applications/Trinityrnaseq

Application Details

• Description: Trinity assembles transcript sequences from Illumina RNA-Seq data.
• Version: 2.2.0, 2.5.1 and 2.8.2
• Modules: trinityrnaseq/gcc/2.2.0, /2.5.1 and /2.8.2
• Licence: Github, open-source

Usage

This represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Briefly, the process works like so:

• Inchworm assembles the RNA-seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.

• Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptional complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs.

• Butterfly then processes the individual graphs in parallel, tracing the paths that read and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that correspond to paralogous genes.

Assemble RNA-Seq data

[username@login] module add trinityrnaseq/gcc/2.8.2
[username@login] Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G 

Find assembled transcripts as: 'trinity_out_dir/Trinity.fasta'

A typical script would be:

#!/bin/bash

if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
    gunzip -c reads.right.fq.gz > reads.right.fq
fi

if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
    gunzip -c reads.left.fq.gz > reads.left.fq
fi

if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
    gunzip -c reads2.right.fq.gz > reads2.right.fq
fi

if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
    gunzip -c reads2.left.fq.gz > reads2.left.fq
fi

#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup --normalize_reads

##### Done Running Trinity #####

if [ ! $* ]; then
    exit 0
fi

Further Information

• https://github.com/trinityrnaseq/trinityrnaseq/wiki

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