Hi!
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.
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.