Which tool is used for RNA-seq analysis?

Which tool is popular to perform RNA-seq analysis, including read mapping, gene/transcript expression level estimation and differential analysis? Here is the survey of which tool to used for RNA-seq analysis.

In summary, the majority will:

• aligns the reads to the genome (or genome+transcriptome) using Tophat;
• count reads using Cufflinks (the second choice is HTSeq-count, which is becoming popular);
• perform differential expression using DESeq/DEXSeq (followed by CuffDiff);
• use Ensemble (followed by Refseq/UCSC) as the annotation resource;
• use GOSeq (followed by IPA and Genego Metacore) for downstream analysis.