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

    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.

  • #2
    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

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