What is it about?
Trinity is a set of tools that allows a researcher to go from raw RNASeq reads to an assembled transcriptome using a simple (but powerful) command-line interface. This paper discusses the way in which the transcriptome is assembled, as well as providing a protocol for how a researcher can generate their own transcriptome and investigate differential expression.
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Why is it important?
Trinity makes a fairly challenging bioinformatics task easy and accessible: assembling sequences de-novo from different transcripts that have wildly different coverage, in such a way that gene isoforms can be linked to each other. Trinity allows researchers to add in additional information (e.g. strand-specific reads and a genome reference) to improve the assembly, but these are not strict requirements for using the platform; in some cases, and especially when coupled with differential expression analysis, the rough "pilot" assembly produced by Trinity can be more than adequate to answer exploratory questions about an organism.
Perspectives
I came across the program when I was working at the Max Planck Institute for Molecular Biomedicine, and was asked to see if I could I used this program to generate a reference transcriptome for Schmidtea Mediterranea while I was working there. This was initially not possible, but I worked out a little tweak to modify (changing to streamed reads from memory-stored reads) it so that it could work on my (fairly high-spec) desktop computer. I also had a go at tweaking Trinity to work with colour-space data from the ABI SOLiD platform, but discovered a few features of colour-space that meant it was probably not a good idea (e.g. polyA and polyT sequences look identical, so chimeric sequences are easily formed).
Dr David A Eccles
Malaghan Institute of Medical Research
Read the Original
This page is a summary of: De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nature Protocols, July 2013, Nature,
DOI: 10.1038/nprot.2013.084.
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