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Old 08-28-2014, 07:20 PM   #1
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Location: Brazil

Join Date: Jul 2014
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Default Best way to compare DEG between de novo pipeline and Cufflinks pipeline


I would like to know your opinion about WHAT IS THE BEST WAY to compare DEG ( Differentialy Expressed Genes) between de novo pipeline ( Trinity ->RSEM(bowtie)-> EdgeR or DESeq ) and Cufflinks pipeline (Cufflinks -> TopHat -> Cuffmerge -> Cuffdiff ).

I know that the output of de novo pipeline is in isoforms level. How I can compare this result with DEGs of Cuffdiff ?

I can do a Blast to make a link between each transcript, but in gene levels, how i do it ?
Clustering ?

Thanks to all.
lucasmiguel is offline   Reply With Quote

cufflinks, de novo, deg, pipeline, trinity

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