Fri, Oct 30, 2015 at 10:12 AM
Customer has RNA-seq data for 6 Arabidopsis samples and 6 wheat samples, and would like to uncover differences in gene expression and possibly in genetics - between the Arabidopsis samples and wheat samples.
Fri, Oct 30, 2015 at 3:19 PM
AccuraScience LB: Unfortunately, the analysis of the Arabidopsis transcriptome and the wheat transcriptome would involve very different analysis pipelines. A reference genome for Arabidopsis is available, thus a reference genome-guided transcriptome assembly pipeline, i.e., Cufflinks would be employed. Although there are some genomic resources available for wheat, a reference genome is not yet available, forcing us to resort to a de novo transcriptome assembly strategy (using Trinity) to analyze the wheat data, and this would be followed by Blast-based annotation of the assembled transcripts. The availability of existing wheat genomic and transcriptomic resources, e.g. the cDNA datasets you referred to, while improves the chance for us to achieve higher quality functional annotation, also leads to increased complexity of the work - e.g., I currently do not have a good idea about what's a proper way of handling cases where a transcript assembled from the RNA-seq data hits multiple resources (e.g. ISGSC and TriFLDB) but the hit sequences have inconsistent annotation.
Additional difficulties for this project include (1) The hexaploid nature of the wheat genome implies that there will be high proportions of ambiguous hits - due to multiple copies of the similar genes resulting from historical genome duplication events (in fact this would be the main reason why a reference genome for wheat has been so difficult to achieve), and (2) The different analysis pipelines applied for the two species (Arabidopsis and wheat) could lead to difficulty in between-species comparison of any results.
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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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