while doing RNA-Seq analysis, after mapping, i have downloaded mouse reference gene set (.gtf format) and did cufflinks analysis to track out FPKM values of the genes. When i did it, i got all the FPKM values '0'. After that, i have edited the reference gene set (.gtf) like this..
1. first i have added a column with name 'chr'.
2.then i merged it with the first column which consisted of chromosome numbers.It came out like chr1, chr2, etc
3.As this was in tabular form, i edited in 'edit attributes' to gtf format.
4.Then i used this .gtf file in cufflinks .
this seemed to worked out. I got FPKM values corresponding to the genes.But i am not sure whether this is the correct way of doing.Please let me know if this is correct, or of not, what is the actual method to do??