My task is to repeat the DATA analysis of RNA-seq data as presented in a journal article using the tophat cufflinks pipeline.

For simplicity Ill just mention the 4 controls

The authors run cufflinks without a reference annotation on each control "to detect possible novel transcripts" --> then cuffmerge on the results --> they then say they run cufflinks again using the merged transctiprts.gtf as the reference annotation. It seems over complicated. 

Cufflinks requires a .BAM file as input but cuffmerge output doesnt give a BAM file....so the only way i can see they did it is by re running cufflinks on every sample for a second time (waste of time?) except this time using the cuffmerge output as the reference annotation. This would mean re running cuffmerge again also afterward.

Surely " to detect possible novel transcripts" doesnt require running cufflinks on everything twice....I mean, isnt this the whole point of cufflinks.

Thanks in advance.
Kenneth
The first Cufflinks run is to generate a new annotation for each sample to discover novel transcripts.
The Cuffmerge run is to merge together all the annotations for each individual sample to create one merged annotation of better quality.
The second Cufflinks run is to quantify the transcripts based on the merged annotation file.

Yes, it is complicated, and the results will contain many false positives.
More importantly, it's generally a waste of time, unless you're working on a poorly annotated genome.
For well-annotated genomes like the mice, human, or drosophila genomes, you shouldn't bother trying to discover novel transcripts.
Just use the most recent annotation available.