title: RNA-seq of Ae. aegypti
design: After receiving assembly files from Azenta, they were imported into ArrayStar along with the Aedes aegypti Liverpool strain AGWG (AaegL5.0) genome FASTA (.fna) and annotation (.gbff) files as the reference genome (Matthews et al., 2018). Two software packages (CLC and Azenta) were used to analyze the transcriptome data. The CLC Genomic Workbench 12.2 software package uses a Local alignment to map sequences to a genome, the trimmed mean of M-values (TMM) to normalize and its own CLC DEG statistical package (Thawng and Smith, 2022). The Azenta software uses the STAR aligner to map, the median-f-ratios to normalize and the DESeq2 for statistical analyses (Thawng and Smith, 2023).