Fig. 3

RNA-seq data processing pipeline. We use FastQC for quality checking, Trimmomatic to remove adapters and low-quality sequences, SAMtools to sort and index sequences, MarkDuplicates to remove duplicates, CollectInsertSizeMetrics to compute the size distribution and read orientation of paired-end libraries, HISAT with Bowtie2 to align the sequences to the human reference genome, and RSEM to quantify and identify differentially expressed genes by aligning reads to reference de novo transcriptome assemblies. Furthermore, our RNA-seq pipeline utilizes an in-house developed software application to automatically parse the outcome files of the pipelines and upload the results into a modeled relational database, which are then used by GVViZ for data annotation, analysis, and visualization