As I often get an inquiry how we do the NGS analysis, especially RNA-seq, so here is what I write it down as my memorandum.
For the outline of the NGS analysis, this web site contains a good summary and video:
Above doesn't talk much about RNA-seq, so I'm including some presentation
The above 2 youtubes are close to what we are actually doing here.
The image is a screenshot of (1) initial bcl2fastq conversion to make fastq files out from HiSeq run directory.