why tophat has library type for paired end?

[jay2008]

hello,
unlike cufflinks,
tophat maps reads to genome without considering strand.
why does tophat need to set library type?

thanks
Yu

[NicoBxl]

Tophat can align strand-specific data also :

--library-type TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. 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.

[jay2008]

tophat generates XS tag. we should not give library type to cufflinks command. is it right?
in other words, if we use fr-firststrand library in tophat, what will happen if we put fr-secondstrand library in cufflinks to the bam file generated by tophat?

[carmeyeii]

i am bumping this up.