GFF model in Tophat and/or Cufflinks?

Question

[manekineko]

Does it makes difference if I provide GFF only to Cuflinks (after the Tophat mapping) or when I provide it to both Tophat and than again to Cufflinks?

Answer 1

[Manvendra Singh]

In TopHat, if you provide GFF, then it would make transcriptome sequence out of it , and maps entire read on it. But at end of the day, it maps segmental reads to the reference genome, so GFF is for guiding the assembly.

I work with junctions so I always go for tophat without providing GFF/GTF then I go for RABT assembly from Cufflinks and then I provide resultant gtf to tophat2 to reassemble.

I see that providing GFF to tophat would improve the quality of mapping.