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Table 1 Software used in this study

From: Systematic evaluation of RNA-Seq preparation protocol performance

software version website reference
Bowtie2 2.1.0 Fast gapped-read alignment with Bowtie 2
TopHat 2.0.10 TopHat: discovering splice junctions with RNA-Seq
HTSeq-count 0.6.1 HTSeq — A Python framework to work with high-throughput sequencing data
edgeR 3.6.1 edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
RSeQC 2.6.4 RSeQC: quality control of RNA-seq experiments
R 3.1.0