Hi,

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.

carol

When you say that you have FeatureCount data, do you mean mean that you have output from the featureCounts() function of the Rsubread package? If so, then the reason that you have multiple rows for the same gene is that your GFF file contains multiple meta-features for the same gene. For example, the meta-features might be Ensembl transcripts, and each gene may have several transcripts that contain almost the same exons.

Thanx Gordon!