Fig. 2.

RNA-seq data processing pipeline. Used 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 size distribution and read orientation of paired-end libraries; HISAT with Bowtie2 to align sequences to the human reference genome; and RSEM to quantify and identify differentially expressed genes by aligning reads to reference de novo transcriptome assemblies