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  • Transcriptome Assembly Questions for Cuffmerge

    Hi. I am trying to run a rather large experiment for my first RNAseq project. Unfortunately, I was convinced to use our SOLiD machines due to cost and proximity (but that's a different issue ). Let's say I get past this and have some mapped reads to input into Cufflinks and then Cuffmerge to make an assembly.

    How many Assembled Transcripts from how many replicate samples are required as input to Cuffmerge to make the final assembly? Do I need to dump ALL of the Assembled Transcripts for each experiment?

    The experiment is using three genotypes (Control, Del, Dup) and three biological replicates per genotype (R1, R2, R3). In addition, we are using both DPSCs and DPSC-neurons for all of these conditions. I said it was big!

    Any help appreciated.

  • #2
    Well, the minimum number would be 2, but you'll want to merge all of the samples involved in any comparison that you intend to make.

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