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  • henriquevf
    Junior Member
    • May 2012
    • 2
    #1

    TopHat and reference genome.

    Hi everyone,
    I have RNA-seq data from a non-model organism without genome sequence and right now I`m trying to use TopHat/Cufflinks for gene expression analysis. The problem is, from what I read so far I need a reference genome for the alignment and I don`t have one, at least for my species. It`s still viable to use tophat, or I should seek another software? Any hints?

    Thank you.
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