So I am pretty new to the bioinformatics movement and am having trouble assembling trancripts using cufflinks with a annotated genome online. I am looking for differential gene expression from an RNA-Seq experiment. I created the annotated genome using Rast (http://rast.nmpdr.org/rast.cgi) and downloaded the files in both GFF and GTF format. I at first had trouble with duplicate ID's so I deleted those using Excel and uploaded the files. When I run the cufflinks program it only outputs 4-6 transcripts. However if I do not use the annotated genome I get thousands but this makes it much harder to analyze down the line. Has anyone used Rast to annotate genomes in this way before or have any idea of where I may have gone wrong?
Also, the genome I'm working with has been annotated in NCBI but I had trouble getting the correct format to use for cufflinks. Suggestions?