Sun, May 10, 2015 at 12:20 PM
Customer has a set of RNA-seq data for a non-model organism (reference genome not available). He wants to have differential expression analysis performed following de novo assembly of the transcriptome.
Sun, May 10, 2015 at 3:59 PM
AccuraScience LB: The current best pipeline for de novo assembly of transcriptomes is the Trinity pipeline (http://www.ncbi.nlm.nih.gov/pubmed/21572440). This work is technically not very challenging, but would require some computational power and running time.
You would probably need some functional annotation work performed for the assembled sequences, because the sequences alone would not offer a lot of useful information for you to develop/test your hypotheses. If so, would you like the annotation done for all genes assembled, or only the differentially expressed genes? The functional annotation can be performed in a relatively straight-forward way, that is, by a Blast search against all relevant sequences, and grabbing the name and annotation of the gene that produces the best hit. Alternatively, it can be done in a more accurate manner, e.g., using Blast2GO (http://www.ncbi.nlm.nih.gov/pubmed/18483572).
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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