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how to determine strand from tophat output for paired-end RNA-seq data

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  • how to determine strand from tophat output for paired-end RNA-seq data

    I used tophat to map paired end seq data xxx.1.fq and xxx.2.fq.
    from the output file, I found most of reads are paired. the flags usually are
    163 - 83
    355 - 403
    99 - 147
    ....
    my question is:
    how to determine the pair is from "+" strand or "-" strand?

    thanks

  • #2
    You probably have figured something out by now but still:
    tophat now has a '-library--type' option which can tell you from which strand the read came from (assuming the library is strand specific).

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