I have some paired end SOLID sequencing data, the protocol using F3/F5
fragments (not the simpler F3/R3).  Both fragments come from the same
strand.  Some of the nuances are explained here:
http://www.biostars.org/p/48597/

Having read the manual for Rsubread, its clear that it can handle SOLID
sequencing, colorspace reads, and paired end sequencing.  However, is the
F3/F5 protocol directly supported, or will there have to be preprocessing
of the F5 fragments?

Simon Coetzee
--
Centro Regional de Hemoterapia
Hospital das Clínicas da Faculdade de Medicina de *Ribeirão Preto
*Universidade de São Paulo

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