Hello all,

I am trying to understand the base detail to analyze RNA-seq data. I followed the nature protocol: which tophat-cufflink-cuffdiff -cummeRbund protocol.

Even though the nature protocol pipeline doesn't use -g option for cufflink, I am wondering whether I'd better use this option since I want to annotate my DEGs.

So I ran two commands. cufflinks with or without -g xxx.gtf file (in my cause mouse gtf file from UCSC)

From the previous link, I knew the role of -g option. (Annotation of miRNA from NGS)

However, I am quite not sure which one is more proper to do the DEG analysis.

Since, when I ran these two commands for cufflink, and then do the cuffdiff-cummeRbund for DEGs, I had differen results. Which one do I have to trust?

Could you please let me know?

Thanks in advance