I want to use cufflinks to do differential expression analysis (8 samples, 4 cases, 4 controls). I have a reference annotation file (refFlat.gtf). In the manual for cuffdiff it states that cuffdiff requires certain attributes (i.e. tss_id, p_id) and that those can be added to the annotation file using the command

cuffcompare -s /path/to/genome_seqs.fa -CG -r annotation.gtf annotation.gtf

When I run this command I get a lot less lines in my annotation file:

[bdeonovic@neon-login-0-2 stoltz]$ wc -l cuffcmp.combined.gtf
35768 cuffcmp.combined.gtf

[bdeonovic@neon-login-0-2 stoltz]$ wc -l refFlat.gtf
78642 refFlat.gtf

Is this necessary? Is there a way to append these cufflink annotations without merging together my gene annotations?