Tophat manual page has listed the general strand-specific protocol:
Library Type | Examples | Description |
fr-unstranded | Standard Illumina | Reads from the left-most end of the fragment (in transcript coordinates) map to the transcript strand, and the right-most end maps to the opposite strand. |
fr-firststrand | dUTP, NSR, NNSR | Same as above except we enforce the rule that the right-most 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 | Ligation, Standard SOLiD | Same as above except we enforce the rule that the left-most 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. |
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