1. Can I use this pipeline to quantify miRNA- or lncRNA-sequencing data?

ANSWER: Yes, if you are interested in quantifying known miRNAs or lncRNAs only, this pipeline can be used. It quantifies any miRNAs or lncRNAs involved in the provided gene annotations files (GTF files). However, if your goal is to discover and quantify novel miRNAs or lncRNAs–which is a common objective in miRNA- and lncRNA-sequencing data analysis–this pipeline does not support novel transcript identification.