Hi there, I'm using featurecounts and I'm wondering if their is a way to get all reads which where not quantified by this software (i.e unassigned reads). I didn't find this option in the Subread documentation.
If it's not possible maybe someone can help me. I try to make a pipeline to analyse smallRNA-seq data. I want to quantify miRNA first on my dataset and then try to quantify other smallRNA (piRNA, snoRNa,...) but I think it would induce some biais if reads quantified as miRNA are still present in the dataset when I'll quantify other smallRNA. Do you think I'm right or not?