TABLE 1.

Library type options for TopHat and Cufflinks.

Library type	RNA-seq protocol	Description
fr-unstranded (default)	Illumina TruSeq	Reads from the leftmost end of the fragment (in transcript coordinates) map to the transcript strand, and the rightmost end maps to the opposite strand
fr-firststrand	dUTP, NSR, NNSR39	Same as above except we enforce the rule that the rightmost end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during first strand synthesis is sequenced
fr-secondstrand	Directional Illumina (Ligation), Standard SOLiD	Same as above except TopHat/Cufflinks enforce the rule that the leftmost end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during second strand synthesis is sequenced