I am using FEELnc to annotate all lncRNAs present in my RNA-Seq samples. But when understanding the results I don't know how to read them. What are the steps to follow after using FEELnc_filter.pl (first step)? Are they all the lncRNAs that match with my RNA-seq samples? To know the name of them do I need to intersect with for example a lncRNA database (lncRBase, http://bicresources.jcbose.ac.in/zhumur/lncrbase/) ?
Or do I need to performe the next two steps and only work with the las output (after FEELnc_classifier.pl)? I am wrong thinking that they only are new or unknown lncRNAs?
Finally is there a tool or something to match each lncRNA with the partner gene or something like a gene ontology site to work with lncRNAs?
Thanks in advance