I am fairly new RNA-seq analysis and recently analyzed my first few datasets. To assign reads from my mapped bam file I used the featureCounts function of Rsubread in R which worked really well with >98% of my reads being assigned to features.
That being said I work in an organism with a genome that may have gaps in its annotation in particular for the type of features that I am interested in. What I am hoping to find out is if there is a way to output the reads that were not assigned to features by featureCounts so that I can take them and process them using another software to determine if there is particular enrichment in certain unannotated regions that may represent novel RNAs that have not been characterized.
Any advice on if this is possible and how to do it would be greatly appreciated. Alternatively if anyone has a suggestion on another way of doing this I would also certainly be open to that!