Dear all

I am new using tophat2 and cufflinks. To my knowledge, one function of cufflinks is to assemble mapped reads into longer parts based on annotation file. I need to find new assembled transcripts that differ from the annotated transcripts or brand new transcripts not been collected in annotation file.

Cufflinks has four output files, among which the transcripts.gtf file seems to be what I am looking for. But I don't know how to achieve my goal. Wish you provide me some advice. THANK you very much!