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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 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Fast gapped-read alignment with Bowtie 2
TopHat 2.0.10 http://ccb.jhu.edu/software/tophat/index.shtml TopHat: discovering splice junctions with RNA-Seq
HTSeq-count 0.6.1 https://htseq.readthedocs.io HTSeq — A Python framework to work with high-throughput sequencing data
edgeR 3.6.1 https://bioconductor.org/packages/release/bioc/html/edgeR.html edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
RSeQC 2.6.4 http://rseqc.sourceforge.net RSeQC: quality control of RNA-seq experiments
R 3.1.0 https://www.r-project.org