Differential Expression Analysis Pipeline with Reference

[pcg]

Hi All,

I am wondering what are people's thoughts on the following way to look for DE genes between samples because cuffdiff does not seem to be summing up the FPKM transcripts scores for each gene. SO because I know the reference genome (human) I am using tophat with the -G option and then running cuffdiff as follows with the human genome annotation file downloaded from ensembl.

cuffdiff hg19.gtf accepted_hits_time1 accepted_hits_time 2

Do I need to go through the entire cufflinks/cuffcompare pipeline or will the above suffice

Many thanks in advancce everyone

[honey]

TopHat with annotation

I read somewhere in the post if you run TopHat with anotation file it will give one gene one row. I have not tried as yet and has same problem.