6.8 years ago by
-G option won't look for novel isoforms. It will simply ignore alignments that are not present in your annotation file. On the other hand -g option will get you the expression estimates for novel isoforms too.
From Cufflinks manual:
-G/--GTF <reference_annotation.(gtf gff)=""> Tells Cufflinks to use the supplied reference annotation (a GFF file) to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.
-g/--GTF-guide <reference_annotation.(gtf gff)=""> Tells Cufflinks to use the supplied reference annotation (GFF) to guide RABT assembly. Reference transcripts will be tiled with faux-reads to provide additional information in assembly. Output will include all reference transcripts as well as any novel genes and isoforms that are assembled.