cuffcompare and cuffmerge

Question

[qudrat]

Hi folks, To find novel transcript in an organism via RNA-Seq, some use Cuffcompare to merge different gtf files produced from Cufflinks while some use Cuffmerge for the same. Please help me to get over this. Thank you

[WouterDeCoster]

I believe (but might be wrong) that you have been told before that the pipeline tophat-cufflinks-cuffmerge is no longer the accepted best pipeline for RNA-seq analysis and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.)