Computational protocol: Disentangling Detoxification: Gene Expression Analysis of Feeding Mountain Pine Beetle Illuminates Molecular-Level Host Chemical Defense Detoxification Mechanisms

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[…] Sequence read information was mapped to the gene models of the male mountain pine beetle genome sequence . Sequence information was converted to fastq format using bam2fastq software (http://www.hudsonalpha.org/gsl/information/software/bam2fastq). The paired-end fastq files were mapped to the genome via CLC Genomics Workbench (http://www.clcbio.com/; CLC bio) using the parameters listed in . The raw RNA-seq data is available at the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) database (accession numbers SRS421461-64) under the TRIA umbrella BioProject (PRJNA169907) that identifies aggregated research project data generated from the TRIA research collaborations on mountain pine beetle systems genomics. [...] The RNA-Seq data were analysed using DESeq package available from The R Project for Statistical Computing (www.r-project.org). The DESeq package calculates differential expression using a negative binomial distribution and a shrinkage estimator for the distribution’s variance. The program calculates fold changes for each gene as well as p-values adjusted (padj) for multiple comparisons using a Benjamini-Hochberg correction . We used a 1% false discovery rate (padj <0.01) to identify transcript accumulation that was significantly different between treatments. The DESeq output is publicly available via figshare. […]

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