I run the Cufflinks assembly tool with known annotation. I dropped the idea of running the tool since it is taking 1-2 days to complete and I have several samples to run. I read in one of the portals that stringtie is efficient and faster so I switched to it. Although it was very quick I see the line number in the assembled transcript file(gtf file) was very less in stringtie when compared to cufflinks. Can you please suggest to me what do the lines represent. Am I losing any data?