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library-type:fr-unstanded vs fisrt-stand vs second-stanrd

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Tophat2:

--library-type The default is unstranded (fr-unstranded). If either fr-firststrand or fr-secondstrand is specified, every read alignment will have an XS attribute tag as explained below. Consider supplying library type options below to select the correct RNA-seq 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.

 

HISAT2:--rna-strandness <string>

Specify strand-specific information: the default is unstranded.
For single-end reads, use F or R. ‘F‘ means a read corresponds to a transcript. ‘R‘ means a read corresponds to the reverse complemented counterpart of a transcript. For paired-end reads, use either FR or RF.
With this option being used, every read alignment will have an XS attribute tag: ‘+‘ means a read belongs to a transcript on ‘+‘ strand of genome. ‘-‘ means a read belongs to a transcript on ‘-‘ strand of genome.

library-type:fr-unstanded vs fisrt-stand vs second-stanrd