I have some Zea mays rna data that I have analised for Differentially expressed genes, aligned with HISAT2,stingtie etc
Now I am interested in identifiying lncRNA sequences out of all the transcripts aligned. My data was polyA enriched, so it´ll be biased but I think it might be interesting to see the result.
Any tips on how to extract the lncRNA out of all the transcripts aligned? I believe that with stringtie files and gffcompare would be possible to extract the lncRNAs but I´m not sure where to start.
Any help is appreciated. Many thanks, Felipe