Is this correct way ??
Question: Is this correct way ??
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'.
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??
This will work for many genomes, but be sure to double check chromosomes such as the mitochrondrial and any unmapped or haplotypes. All identifiers must be exactly the same for most tools.