I would appreciate if let me know how is better to specify feature type of featureCounts. actually I am not sure about that, because by default is exon, but I want to count genes and transcripts (according to 3rd column in GTF file) on sam files, so I got mixed up I have to define feature type as gene (meta feature) or exon or what else? and what does meta features mean? it means the aggregate of all features or just based on gene count?
does anybody have a suggestion?
thanks in advance