I am working on mRNA human Tumor gene Expression. I ran tophat followed by cufflinks using hg 19 reference..
Now i wish to annotate the output of cufflinks with the mRNA gtf file.
My doubts are.. 1. should i Map my data with mRNA.fa or hg19 reference while running tophat?? 2. could you suggest me to get the mRNA gtf file??
i tried downloading the mRNA gtf file from ucsc table browser as mentioned below..
Group: Genes and gene Prediction Track Track:Refseq Genes Table:Humanmrna(all_mrna)
the output file size is around 200MB. But i heard known mRNA are only 22000.
Could you Suggest me to get the mRNA.gtf file and the reference to be used during mapping??