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 | 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 | RSeQC: quality control of RNA-seq experiments | |
R | 3.1.0 | Â |