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Old 02-14-2013, 09:25 PM   #1
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Location: South Korea

Join Date: Jun 2009
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Default 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 at 09:28 PM.
dolsemtl is offline   Reply With Quote

cuffcompare, cufflinks, gene expression profiling, gene model, rna-seq

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