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.