A flexible Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes

We developed a Transcriptomic Analysis Pipeline (TAP) as a flexible workflow for comprehensive transcriptome analysis from any species with a reference genome. We tested TAP in a case study to compare polyA+ and rRNA-depletion RNA-seq library protocols using Drosophila melanogaster following different thermal stress temperatures. TAP provides a flexible and complete pipeline to enable researchers to extract more biologically relevant interpretations by integrated and interactive transcriptome analysis. Adult flies were subjected to 5 different temps with 3 biological replicates, total RNA extracted and used to construct polyA-selected and rRNA-depleted RNA-Seq libraries.