Confused between training input and prediction input
I am using augustus web server to predict genes. I have trained augustus using verified ORFs also provided cDNA sequences while training. As an output of training I got optimised parameter for my gene structure. Along with that, I also got predicted genes (both ab initio and with hints) from supplied genome file with the newly optimized AUGUSTUS parameters. Till now everything is fine.
My question is as I already got predicted genes ab initio and with hints, do I need to run prediction as well. ?
For a try I also did prediction with the parameter which I got after training. Again I supplied same cDNA file which I supplied with training program. As an output I got gene structure but the number of genes predicted this time is not matching with number of genes I got after training algorithm.
Kindly help me to solve this confusion. I am using cufflink generated transcripts as cDNA file.