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  • cufflinks's gene model options

    Hi all,

    I am going to use cufflinks for gene exprssion profiling in my RNA-seq analysis.
    There are two way to work gene expression profiling against known gene model.
    1) running cufflinks with -G option
    2) running cufflinks without options related to gene model -> running cuffcompare with known gene model

    Is there anyone who has exprience of running two workflows and comparing the results of gene expression profiling? I wonder if the results from two workflows are same.
    If no, which workflow is showing better result?

    Thanks for any comments
    Last edited by dolsemtl; 02-14-2013, 10:28 PM.

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