CuffDiff input: Transcripts and Bias Correction Reference

[skmotay]

In Cuffdiff in Galaxy, the first input is "transcripts." Then the inputs are for different conditions and replicates. Then for Bias Correction, there is an input for Reference Sequence data. I'm looking for clarification on what these are/how they're different.

I see that "transcripts" can be generated from cuffcompare, but should I use a known reference transcriptome if it's available? I found these as csv files.

I'm using Drosophila RNAseq data generated from a specific tissue. Should I use the reference transcriptome from that tissue? (it's available as a fastq file).