I was just wondering if it happened to you guys before. There are some genes I can clearly see they are expressed from the wig file (The hight are as high as 50 in almost all the exons). But cufflinks didn't give me any values for these genes. I used -G option with mm9 assembly.
I guess what I am trying to say is even cufflinks gives you some gene expression as 0, you still need to go to the genome browser to double check everything.
I guess what I am trying to say is even cufflinks gives you some gene expression as 0, you still need to go to the genome browser to double check everything.