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 |