Difference between revisions of "Trinity Protocol"
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Revision as of 18:08, 18 January 2016
This is the Trinity protocol for assembling transcriptomes
Timing
Steps 1–3, collection of RNA-seq data: ~10 min Steps 4–7, Trinity de novo transcriptome assembly of 4 million paired-end Illumina reads: 60–90 min Steps 8–13, quality assessment (optional): ~90 min Steps 14–18, using RSEM for abundance estimation: 40–60 min Steps 19–25, differential expression analysis using EdgeR: <5 min Step 26 (optional): variable Step 27, automation of required sections: 2–3 h
The time taken for each of the commands executed for the required sections of the tutorial, as reported during the automated execution via ‘run_Trinity_edgeR_pipeline.pl’ described above, and as run on a high-performance server at the Broad Institute (hardware specifications included), is provided in the Supplementary Note.
