RNA-seq analysis pipeline for human genome

Multiplexed Illumina sequencing data were demultiplexed using Illumina bcl2fastq converter (version 2.20.0.422). Reads were aligned on the Homo sapiens genome (Build version GRCh38, NCBI) using Hisat2 (Kim et al, 2015 (link)) (version 2.2.1) with the default settings. After alignment, reads mapping to annotated protein‐coding genes were counted using featureCounts (version 2.0.1). Annotations were obtained from the Ensembl release 100. Counted reads for protein‐coding genes were used for differential expression analysis using the R/Bioconductor package DESeq2 (Love et al, 2014 (link)) (version 1.26.0).