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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

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