Chapter 6 Transcriptomics data set

The transcriptomics dataset comes from a subset of the data from (Ayala-Ortiz et al. 2021) which includes only male Nicrophorus pustulatus under starved and fed conditions.

Burying beetle (Nicrophorus pustulatus). Photo by Chris Joll (2018)

Figure 6.1: Burying beetle (Nicrophorus pustulatus). Photo by Chris Joll (2018)

Because there was no reference genome for Nicrophorus pustulatus, mRNA reads counts were obtained using the pseudoaligner Kallisto (Bray et al. 2016)

6.1 Importing kallisto pseudocount data

Kallisto pseudocounts are loaded using the package tximport.

library(tidyverse)
library(tximport)
library(readr)

metadata <- read_csv('data/metadata_nicrophorus.csv')
files <- file.path('data', 'nicrophorus_counts', metadata$SampleID, "abundance.h5")
names <- metadata$SampleID

txi.kallisto <- tximport(files, type = 'kallisto', txOut = TRUE)

References

Ayala-Ortiz, Christian O, Jacob W Farriester, Carrie J Pratt, Anna K Goldkamp, Jessica Matts, W Wyatt Hoback, John E Gustafson, and Darren E Hagen. 2021. “Effect of Food Source Availability in the Salivary Gland Transcriptome of the Unique Burying Beetle Nicrophorus Pustulatus (Coleoptera: Silphidae).” Plos One 16 (9): e0255660.
Bray, Nicolas L, Harold Pimentel, Páll Melsted, and Lior Pachter. 2016. “Near-Optimal Probabilistic RNA-Seq Quantification.” Nature Biotechnology 34 (5): 525–27.