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  • Dose Cufflinks work on bacterial RNA-seq ?

    Dear all,

    I am a new one who getting start in RNA-seq area.

    I have read the Cufflinks's paper and known it's a reference base assembler.

    And Now, I have two dataset.
    1. a bacterial genome assembled by Ray (denovo assembly)
    2. 3 condition of this bacteria of RNA-seq.

    I am wondering can I use the denovo-genome as a reference and use predicted ORF (from genome) as guild-transcript to run Cufflinks?

    Dose the process get any problem?

    Thanks a lot
    James

  • #2
    Dear James,

    I hope that I can help you!

    I don't recommend Cufflinks for bacterial rna-seq tech, you can use it... And in fact it works pretty well.

    There are other programs that you can check out like EDGE-Pro and Rockhopper. Actually I recommend that you use all of them and compare the results..

    I haven't worked with de novo assembly, but I think you can use ray output to use as your reference genome... Other people here can help you further

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