I have aligned raw RNA-seq reads to the Ensembl reference genome. I intend to quantify the expression using FeatureCounts of only say lincRNAs. What would be a better approach, use the full GTF file containing all types of RNAs or create a GTF containing only lincRNA and then use as input for FeatureCounts?
I tried both these approaches. For protein coding and lncRNA, the results were similar but a huge difference in case of miRNA.