Question: Cufflinks With Gtf File
gravatar for geek_y
6.8 years ago by
geek_y11k wrote:


I am working with cufflinks,cuffdiff for RNA-SEQ data.

In cufflinks, If we are not looking for novel isoforms, we need to use GTF file with cufflinks ( -G GTF ).

My question is that if we do not want any novel isoforms, we can skip the cufflinks step in Tuxedo protocol. We can use TopHat and cuffdiff to get differential isoforms. But in that case why cufflinks has an option for -G GTF.

gtf cufflinks tophat2 • 2.9k views
ADD COMMENTlink modified 6.8 years ago by andrew.j.skelton736.1k • written 6.8 years ago by geek_y11k
gravatar for andrew.j.skelton73
6.8 years ago by
andrew.j.skelton736.1k wrote:

What if an isoform exists in the reference genome but not in your sample?

ADD COMMENTlink written 6.8 years ago by andrew.j.skelton736.1k
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