Does tophat use the library-type information for mapping, or just for the XS flag?

[carmeyeii]

Hi all, quick question:

When I specify library-type to TopHat, i.e., first-strand, second-strand, unstranded, TopHat appends a value + or - to the XS:A tag, which is useful for subsequent analyses, such as annotation.

However, does this information influence the "mappability" of reads, or is this unaffected?

Carmen

--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.

[carmeyeii]

My guess is that the information will be considered for mapping reads to the GTF file if supplied with -G . In that dataset, read pairs should be concordant with transcript strand. i,e., if -library-type first-strand was indicated, and transcript A is at coods. X to Y, + strand, read of the mate pair should map to the reverse-complement of the 3' end of TRANSCRIPT A, and READ 2 of the mate pair should map to the 5' end, in the same orientation as the transcript sequence.

However, if no GTF is supplied with -G, or in the subsequent stage of mapping reads that didn't map to the transcriptome, now to the whole genome, then TopHat should make no use of library-type information, right?

Thanks,
Carmen