So im very new to this whole deal, and very new to computer science stuff in general. I trying to do RNA seq computation and seem to be running into an unusual problem (i think). I am running Slurm jobs in the terminal and my end results are weird. The job is a whole pipeline using bowtie2, then tophat, then cufflinks, cuff quant, and then featurecounts and cuff norm. The idea is to take the raw counts from featurecounts and use it in edgeR. I run cuffnorms at the end to get FPKM counts, just to get an idea before starting edgeR. I noticed that feature counts is outputting counts with about 25,000 gene or features, yet cuffnorms is outputing 57,000 gene or features. The whole pipeline is using the same .gff3 and .fa files from ensembl (mouse). Does anyone know why this is happening?