Mon, Jun 29, 2015 at 5:07 AM
Customer inquires about RNA-seq data analysis project for a fish species.
Mon, Jun 29, 2015 at 8:16 AM
AccuraScience LB: A key question for RNA-seq data analysis project is whether a reference genome and proper gene annotation is available for the species. If a reference genome of reasonable quality is available, the Cufflinks pipeline would be proper to use for the analysis. If, on the other hand, a quality reference genome (and proper gene annotation) is not available, then the Trinity pipeline has been used to assemble the transcriptome de novo, with the additional gene annotation work, which would be a much more involving project.
I did a quick search, and found that the species of interest has been recently sequenced. However, (1) I am not sure how readily available the genome sequence is - we would need to be able to download it in order to run Cufflinks, (2) The focus of the paper in which this genome project was reported was on evolution insights, i.e., historical whole-genome duplication events - rather than the genome itself, raising concerns about how well the gene annotation has been made for this genome, and (3) This issue with gene annotation is made more severe considering the historical whole-genome duplication events discussed in the paper, because each time the genome duplicates itself, each gene is duplicated, which adds to the difficulty in precisely defining those genes and annotate them properly.
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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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