Inserts and sequencing strategies

You can retrieve three different informations :

1. The relative orientation of reads :
   • I : Inwards
   • M : Matching
   • O : Outwards
2. The strandedness of the library :
   • S : Stranded
   • U : Unstranded
3. The strand origin of reads :
   • F : read 1 (or single-end read) comes from the forward strand
   • R : read 1 (or single-end read) comes from the reverse strand

in practice, with Illumina paired-end RNAseq protocols you will either deal with:

Unstranded RNAseq data

IU type from above. Also called fr-unstranded in TopHat/Cufflinks nomenclature

Stranded RNAseq data produced with Illumina TrueSeq RNAseq kits

ISR type from above or fr-firststrand in TopHat/Cufflinks nomenclature