18 months ago by
The dataset/file formats are described here under the sections named like "Differential splicing tests - XXX": http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
Scientific details are also covered under this RNA-seq tutorial: https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq
Promoter differential expression file questions:
does it lists no. of genes using common promoter? - Each gene is listed distinctly. Different genes do not share a common promoter site - instead, the transcripts associated with the same promoter will be grouped into the same gene by the tool, the supplied reference annotation, or both (depending on the parameters/inputs)
what does the fpkm value shows..is it for the promoter? - FPKM is calculated for four classes of features (promoter is not included independently as it is covered by the gene differential expression test). See the section "Differential expression tests" in the first (manual) link above.
similarly the splice junction diff expn file..what does each junction represent? - A splice site present in the input NGS reads used to create transcripts/isoforms, the supplied reference annotation, or both (also depends on the parameters/inputs)
Hopefully this helps! Jen, Galaxy team