I'm completely new to RNASeq analysis so I'm having a lot of difficulties analyzing the data. First of all, I got some raw FeatureCount data, and there are multiple entries of the same meta-feature (gene) all with the same or very similar counts. What does this mean? How do I combine them or remove them so that I only have data for one meta-feature (gene)?
Also, the raw data includes novel unannotated "genes". How do I remove these so that I can analyze only the annotated genes (ie. ones in Ensembl).
Any help or advice would be greatly appreciated. Thanx.