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  • skm
    Junior Member
    • Nov 2011
    • 5
    #1

    cuffmerge assembly vs denovo assembly of RNAseq data

    Hi all,

    I have RNAseq data of stress-control of various tissue of a plant. I am doing differential gene expression. In addition, cuffmerge provides me with transcripts assembled. But is this a valid transcriptome at publication ? Or should I go for a denovo assembly of the RNAseq data ? and for a comprehensive assembly of all the tissues together ?

    I have not come across publications reporting cuffmerge transcriptome.

    please advise.

    Thanks

    regards
    skm
    Tags: assembly, cuffmerge, rnaseq
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