Last update of the drawing 2019/08 (Cf. GUESSmyLT):
Original post: I tried to review the meanings of the different RNA-seq library types because it's often confusing and hard to understand/know what they are despite their importance in downstream analyses.
I would be glad to get some comment/correction/criticims and complementary information, to make the resource the most exhaustive as possible. Given the numerous question about RNA-seq library type I found on internet I'm sure this small contribution could be useful not only for me but for a broad audience.
Here are nice resources amongst others I found by googling:
I summarised the result in these figures:
And here is the few information I found about which technologies produces them:
--fr orientation are produced using the Illumina paired end protocol.
--fr-firststrand dUTP, NSR, NNSR
--fr-secondstrand Ligation, Starndard SOLiD
--rf orientation are produced using the Illumina mate-pair protocol.
--ff orientation are produced in using the SOLiD mate-pair protocol. It also the case for Roche 454 paired-end libraries (these are called paired-end, but are based on the same principles as the mate-pair libraries)
Extra information not necessarily obvious for everybody: f mean forward and r reverse. Consequently --fr means forward reverse and --rf means reverse forward.
Trinity doesn't use the same referrntiel (it uses the DNA) so RF corresponds to fr-firststrand and FR to fr-secondstrand.