I have run the cufflinks with gtf guided parameter (-g). But most of my transcripts are not matching to the gtf transcripts. I have checked the address of cuffinks generated genes and it is match to some corresponding genes in reference gtf file. Some how I was able to found that most of the trancripts which does not match to the reference gtf has multiple transcripts, because the blast results of these transcripts generates multiple hits (usually 2 or 3).
I dont understand why the trancripts generated by cufflinks has more than one transcripts.
Kindly help and thanks in advance