I am having trouble getting Cufflinks v2.2.1. output. I have run cufflinks with reference annotation file and got the reasonable results . In order to find the potential novel isoform ,I run cufflinks without any reference annotation file but cufflinks output only contained the information of chr1 and the transcript.gtf file is not readable.
I am wondering if anybody met the same problem before and what is the solution?
thanks in advance