RNA-seq Data Analysis for Samples of Mixed Species (7/29/2015)


Wed, Jul 29, 2015 at 7:18 PM

Customer describes a RNA-seq data analysis project involving samples isolated from the root nodules of soybean plants. The samples are a mixture of two species: soybean and the nitrogen-fixing bacterium Bradyrhizobium. She would like differential expression analysis to be performed across two groups of samples.

Wed, Jul 29, 2015 at 7:36 PM

AccuraScience LB: Although the reference genomes for both species are available, this project presents some unique challenges: (1) when a read is mappable to both soybean and Bradyrhizobium genome, how to handle it, (2) different samples likely have different soybean vs. Bradyrhizobium ratios, how to quantify/benchmark this ratio before performing the differential expression analysis.

For (1), a straight-forward strategy that should be tried first is to merge the two genomes into a single super-genome, i.e., regarding the bacterial genome as a special additional chromosome in the soybean genome.

For (2), we should either use the total number of reads mappable to either genome for benchmark purposes, or try to use some well-characterized "house-keeping" genes in both species.

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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.

Disclaimer: This text was selected and edited based on genuine communications that took place between a customer and AccuraScience data analysis team at specified dates and times. The editing was made to protect the customer's privacy and for brevity. The edited text may or may not have been reviewed and approved by the customer. AccuraScience is solely responsible for the accuracy of the information reflected in this text.