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  • What is the difference between Cufflinks and other packages

    Hi:

    I have naive question and hope I could get an answer here.

    What is the difference between Cufflinks and other softwares such as edgeR, ERANGE.

    My aim is :

    I have RNA-Seq data from 5 cancer samples and 5 normal samples. (10 are different people).

    I want to have :
    a. alternative splicing events and novel isoforms.
    b. Gene expression differences between known transcripts.

    cufflinks - can identify novel transcripts (through assembly) and estimates abundance of transcripts and computes differential RNA levels.


    edgeR - is an R package that can compute differential expression of known transcripts between 5 cancer and 5 normal samples.
    edgeR cannot assemble novel transcripts and calculate their abundance.


    question:

    Can Cufflinks give me the differential expression between known and novel transcripts between 5 cancer and 5 normals. And can this be comparable to edgeR. The methodology is different for both.

    Cuffdiff - Although cuffdiff is designed to compare relative abundance between samples, can we define [T1,T2,T3,T4,T5] and [N1,N2,N3,N4,N5] samples as two blocks. I am not sure how cuffdiff will compare 5 normals and 5 tumors.



    Any help is deeply appreciated as I am very much confused. May be I have the gene expression (LIMMA) hangover !

    thank you.

    Adrian
    Last edited by adrian; 04-07-2011, 03:13 PM.

  • #2
    The current version of Cufflinks supports replicates for comparison.

    Comment


    • #3
      You could perform novel transcript assembly using cufflinks, merge with known genes using cuffcompare and then use the resulting annotation as gene definitions to use in an edgeR workflow

      Comment

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