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  • Cufflinks library-type for SOLiD strand specific single data

    I have SOLiD strand specific single reads and am using Cufflinks(0.9.1) and Tophat(1.1.1).

    Cufflinks help page says library-types are the following
    illumina-stranded-paired-end
    illumina-stranded-single-end
    illumina-unstranded (default)
    solid-paired-end
    solid-single-end

    Which library-types should I use to utilize strand information ?

    thanks

  • #2
    This set up will actually be changing soon (probably today) with a new release of Cufflinks. The manual should be able to provide you with information on which library-type option to use. It will most likely be "fr-secondstrand". Do you know if your reads should map to the transcript strand or opposite strand?

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